From 354132e8874185bce6228d55b0489303ee0abc2f Mon Sep 17 00:00:00 2001
From: endergebnis <endergebnis@hanime.zip>
Date: Fri, 4 Sep 2026 02:43:00 +0200
Subject: [PATCH] =?UTF-8?q?Initial=20commit:=20rustytokens=20=E2=80=94=20n?=
 =?UTF-8?q?ative=20codebase=20indexer=20+=20MCP=20server?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
---
 .gitignore                          |   1 +
 Cargo.lock                          | 591 ++++++++++++++++++++++++++++
 Cargo.toml                          |  22 ++
 README.md                           | 172 ++++++++
 src/cli.rs                          | 107 +++++
 src/config.rs                       |  81 ++++
 src/ctags/mod.rs                    |  65 +++
 src/discovery/mod.rs                |  59 +++
 src/graph/mod.rs                    | 177 +++++++++
 src/index/hashing.rs                |  23 ++
 src/index/imports.rs                | 398 +++++++++++++++++++
 src/index/mod.rs                    |   5 +
 src/index/pipeline.rs               | 209 ++++++++++
 src/index/schema.rs                 |  71 ++++
 src/index/store.rs                  | 311 +++++++++++++++
 src/main.rs                         |  81 ++++
 src/mcp/mod.rs                      | 254 ++++++++++++
 src/ops.rs                          | 341 ++++++++++++++++
 src/output.rs                       | 100 +++++
 src/search/mod.rs                   | 130 ++++++
 tests/cli.rs                        | 480 ++++++++++++++++++++++
 tests/fixtures/cdemo/dead.c         |   1 +
 tests/fixtures/cdemo/main.c         |   5 +
 tests/fixtures/cdemo/util.c         |   3 +
 tests/fixtures/cdemo/util.h         |   1 +
 tests/fixtures/cppdemo/main.cpp     |   5 +
 tests/fixtures/cppdemo/math.cpp     |  13 +
 tests/fixtures/cppdemo/math.hpp     |  11 +
 tests/fixtures/htmldemo/app.js      |   1 +
 tests/fixtures/htmldemo/index.html  |  10 +
 tests/fixtures/htmldemo/style.css   |   1 +
 tests/fixtures/javademo/Dead.java   |   5 +
 tests/fixtures/javademo/Main.java   |  15 +
 tests/fixtures/javademo/Util.java   |   5 +
 tests/fixtures/pydemo/dead.py       |   2 +
 tests/fixtures/pydemo/main.py       |   5 +
 tests/fixtures/pydemo/util.py       |   2 +
 tests/fixtures/rustdemo/src/dead.rs |   1 +
 tests/fixtures/rustdemo/src/lib.rs  |   5 +
 tests/fixtures/rustdemo/src/main.rs |   5 +
 tests/fixtures/rustdemo/src/util.rs |   3 +
 tests/fixtures/tsdemo/a.ts          |   3 +
 tests/fixtures/tsdemo/b.ts          |   3 +
 43 files changed, 3783 insertions(+)
 create mode 100644 .gitignore
 create mode 100644 Cargo.lock
 create mode 100644 Cargo.toml
 create mode 100644 README.md
 create mode 100644 src/cli.rs
 create mode 100644 src/config.rs
 create mode 100644 src/ctags/mod.rs
 create mode 100644 src/discovery/mod.rs
 create mode 100644 src/graph/mod.rs
 create mode 100644 src/index/hashing.rs
 create mode 100644 src/index/imports.rs
 create mode 100644 src/index/mod.rs
 create mode 100644 src/index/pipeline.rs
 create mode 100644 src/index/schema.rs
 create mode 100644 src/index/store.rs
 create mode 100644 src/main.rs
 create mode 100644 src/mcp/mod.rs
 create mode 100644 src/ops.rs
 create mode 100644 src/output.rs
 create mode 100644 src/search/mod.rs
 create mode 100644 tests/cli.rs
 create mode 100644 tests/fixtures/cdemo/dead.c
 create mode 100644 tests/fixtures/cdemo/main.c
 create mode 100644 tests/fixtures/cdemo/util.c
 create mode 100644 tests/fixtures/cdemo/util.h
 create mode 100644 tests/fixtures/cppdemo/main.cpp
 create mode 100644 tests/fixtures/cppdemo/math.cpp
 create mode 100644 tests/fixtures/cppdemo/math.hpp
 create mode 100644 tests/fixtures/htmldemo/app.js
 create mode 100644 tests/fixtures/htmldemo/index.html
 create mode 100644 tests/fixtures/htmldemo/style.css
 create mode 100644 tests/fixtures/javademo/Dead.java
 create mode 100644 tests/fixtures/javademo/Main.java
 create mode 100644 tests/fixtures/javademo/Util.java
 create mode 100644 tests/fixtures/pydemo/dead.py
 create mode 100644 tests/fixtures/pydemo/main.py
 create mode 100644 tests/fixtures/pydemo/util.py
 create mode 100644 tests/fixtures/rustdemo/src/dead.rs
 create mode 100644 tests/fixtures/rustdemo/src/lib.rs
 create mode 100644 tests/fixtures/rustdemo/src/main.rs
 create mode 100644 tests/fixtures/rustdemo/src/util.rs
 create mode 100644 tests/fixtures/tsdemo/a.ts
 create mode 100644 tests/fixtures/tsdemo/b.ts

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+checksum = "7da8b5736845d9f2fcb837ea5d9e2628564b3b043a70948a3f0b778838c5fb4f"
+
+[[package]]
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+version = "2.0.119"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "872831b642d1a07999a962a351ed35b955ea2cfc8f3862091e2a240a84f17297"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "unicode-ident",
+]
+
+[[package]]
+name = "syn"
+version = "3.0.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e6275cddf4610d1775e6d1fe9469b2e77d0f39fd98fb7450901b821e0c53649f"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "unicode-ident",
+]
+
+[[package]]
+name = "unicode-ident"
+version = "1.0.24"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e6e4313cd5fcd3dad5cafa179702e2b244f760991f45397d14d4ebf38247da75"
+
+[[package]]
+name = "utf8parse"
+version = "0.2.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "06abde3611657adf66d383f00b093d7faecc7fa57071cce2578660c9f1010821"
+
+[[package]]
+name = "vcpkg"
+version = "0.2.15"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426"
+
+[[package]]
+name = "version_check"
+version = "0.9.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0b928f33d975fc6ad9f86c8f283853ad26bdd5b10b7f1542aa2fa15e2289105a"
+
+[[package]]
+name = "walkdir"
+version = "2.5.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "29790946404f91d9c5d06f9874efddea1dc06c5efe94541a7d6863108e3a5e4b"
+dependencies = [
+ "same-file",
+ "winapi-util",
+]
+
+[[package]]
+name = "winapi-util"
+version = "0.1.11"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c2a7b1c03c876122aa43f3020e6c3c3ee5c05081c9a00739faf7503aeba10d22"
+dependencies = [
+ "windows-sys",
+]
+
+[[package]]
+name = "windows-link"
+version = "0.2.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f0805222e57f7521d6a62e36fa9163bc891acd422f971defe97d64e70d0a4fe5"
+
+[[package]]
+name = "windows-sys"
+version = "0.61.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ae137229bcbd6cdf0f7b80a31df61766145077ddf49416a728b02cb3921ff3fc"
+dependencies = [
+ "windows-link",
+]
+
+[[package]]
+name = "xxhash-rust"
+version = "0.8.18"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "aee1b19627c7c60102ab80d3a9cbe18de90bfe03bfa6c3715447681f0e8c8af6"
+
+[[package]]
+name = "zerocopy"
+version = "0.8.56"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "556764e583adb45a9f8d413c2a147fa7e8d821e48e12b14fd560b607998b75eb"
+dependencies = [
+ "zerocopy-derive",
+]
+
+[[package]]
+name = "zerocopy-derive"
+version = "0.8.56"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f2ab42fc20575779bd240faa45f94a74256f755c0fa9e89f0ede20d91d0cdfc1"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.119",
+]
+
+[[package]]
+name = "zmij"
+version = "1.0.23"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "29666d0abbfad1e3dc4dcf6144730dd3a3ab225bbbdac83319345b1b44ccfc1b"
diff --git a/Cargo.toml b/Cargo.toml
new file mode 100644
index 0000000..441e039
--- /dev/null
+++ b/Cargo.toml
@@ -0,0 +1,22 @@
+[package]
+name = "rustytokens"
+version = "0.1.0"
+edition = "2024"
+
+[dependencies]
+clap = { version = "4", features = ["derive"] }
+rusqlite = { version = "0.31", features = ["bundled"] }
+ignore = "0.4"
+rayon = "1"
+xxhash-rust = { version = "0.8", features = ["xxh3"] }
+serde = { version = "1", features = ["derive"] }
+serde_json = "1"
+anyhow = "1"
+regex = "1"
+
+[dev-dependencies]
+serde_json = "1"
+
+[profile.release]
+lto = true
+strip = true
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..672d313
--- /dev/null
+++ b/README.md
@@ -0,0 +1,172 @@
+# rustytokens
+
+A native Rust CLI + MCP server that indexes a codebase with
+[`universal-ctags`](https://github.com/universal-ctags/ctags) and lets an AI
+coding agent retrieve **symbols and functions** instead of whole files — saving
+context tokens.
+
+Language coverage (via ctags): Rust, Java, Python, C/C++, TypeScript,
+JavaScript, HTML. HTML import edges are extracted directly (not via ctags), and
+`<link>`/`<script>`/`<img>` references to local `.css`/`.js`/image files are
+tracked as imports. CSS files are discovered and import-tracked, but ctags has
+no CSS parser — `search symbols` returns nothing for `.css` files.
+
+`rustytokens` is an independent, clean-room implementation. It does not share
+code with any AGPL-licensed project.
+
+## Prerequisites
+
+- Rust (MSRV: current stable; built and tested on nightly)
+- `universal-ctags` on `PATH` (`ctags --version` must report Universal Ctags)
+
+```bash
+# Debian/Ubuntu
+sudo apt install universal-ctags
+# macOS
+brew install universal-ctags
+```
+
+No system SQLite needed — `rusqlite` bundles SQLite with FTS5.
+
+## Build
+
+```bash
+cargo build --release
+# binary at target/release/rustytokens
+```
+
+## Commands
+
+| Command | Purpose |
+|---|---|
+| `index create <path>` | Index a project from scratch |
+| `index update <path>` | Re-index only changed files (content-hash diff) |
+| `search symbols <query>` | Symbol search by name (exact > prefix > full-text) |
+| `search text <query>` | Full-text search over file contents |
+| `inspect symbol <id>` | Source of a single symbol |
+| `inspect outline <file>` | Symbol outline of a file |
+| `inspect file <file> [--lines a-b]` | Read a file or line range |
+| `inspect tree [--depth n]` | Indexed file tree |
+| `inspect blast-radius <file> [--depth n]` | Files transitively affected by a change |
+| `find importers <file>` | Who imports this file |
+| `find dead` | Files nobody imports (entry points excluded) |
+| `inspect cycles` | Circular imports |
+| `serve` | MCP server over stdio |
+| `stats` | Index statistics |
+
+Global options: `--project <dir>` (default `.`), `--format json|table`
+(default `json`), `--compact`.
+
+## Examples
+
+```bash
+# Index a project
+rustytokens index create ./myproject
+
+# Find the `authenticate` function
+rustytokens --project ./myproject search symbols authenticate
+
+# Get only that function's source (id from the search result)
+rustytokens --project ./myproject inspect symbol 42
+
+# Which files import auth.rs?
+rustytokens --project ./myproject find importers src/auth.rs
+
+# What's dead / circular?
+rustytokens --project ./myproject find dead
+rustytokens --project ./myproject inspect cycles
+
+# Human-readable output
+rustytokens --project ./myproject --format table search symbols authenticate
+```
+
+## MCP integration
+
+Register the binary as a stdio MCP server (e.g. in Claude Code / Finir
+`mcp.json`):
+
+```json
+{
+  "mcpServers": {
+    "rustytokens": {
+      "command": "/path/to/rustytokens",
+      "args": ["--project", "/path/to/your/project", "serve"]
+    }
+  }
+}
+```
+
+Exposed tools: `index_create`, `index_update`, `search_symbols`,
+`search_text`, `inspect_symbol`, `inspect_outline`, `inspect_file`,
+`inspect_tree`, `find_importers`, `find_dead`, `inspect_cycles`,
+`inspect_blast_radius`, `stats`.
+
+## Why it saves tokens
+
+Instead of sending a whole file, the agent fetches only the symbol it needs.
+Measured on `rustytokens`' own `src/ops.rs` (396 lines, ~11.7 KB):
+
+- Whole file: 396 lines, 11,675 chars (~2,900 tokens)
+- `inspect symbol` for `build_tree`: 14 lines, 437 chars (~110 tokens)
+
+That single retrieval is ~96% smaller than reading the file. Across a large
+codebase and a long session, per-symbol retrieval keeps context focused on the
+code actually being edited.
+
+## Performance
+
+Measured on a Xeon E5-2667 v3 @ 3.2 GHz (16 cores), `cargo build --release`,
+`universal-ctags` on `PATH`. Wall time, CPU time and peak RSS via
+`/usr/bin/time -v`.
+
+| Operation | Repo (files) | Wall | CPU | Peak RSS |
+|---|---|---|---|---|
+| `index create` | nlohmann/json (497) | 1.61 s | 0.98 s | 22 MB |
+| `index create` | gson (264) | 0.92 s | 0.46 s | 13 MB |
+| `index create` (warm) | nlohmann/json (497) | 1.55 s | — | — |
+| `index update` (no-op) | nlohmann/json (497) | 0.02 s | — | — |
+| `search symbols` | — | 8.7 ms | — | 7.8 MB |
+| `find dead` | — | 4.4 ms | — | — |
+| `inspect cycles` | — | 3.7 ms | — | — |
+
+Notes:
+
+- `index update` is ~50× faster than a full rebuild when nothing changed: it
+  hashes every file in parallel (rayon) and re-indexes only changed ones, while
+  `index create` drops and rebuilds the whole database. A warm `index create`
+  (≈1.55 s) shows that hashing dominates the cost.
+- Hardware cycle counters were not available (`perf` tools missing on this
+  kernel), so cycle figures are estimates: CPU time × 3.2 GHz nominal.
+
+## Development
+
+```bash
+cargo fmt
+cargo clippy
+cargo test --release   # unit (in-memory SQLite) + CLI integration tests
+```
+
+Test fixtures live in `tests/fixtures/` (own small Rust/Python/TS repos).
+
+## Licensing
+
+`rustytokens` is an independent, clean-room implementation — no code is taken
+from any AGPL-licensed project, so the project's own source is yours to license
+however you choose (MIT, proprietary, commercial, closed-source). Decide and
+set it once: add a `license` field to `Cargo.toml` and, if you ship the source,
+drop in a `LICENSE` file.
+
+Dependencies are all permissive (MIT / Apache-2.0 / BSL-1.0 / Unlicense):
+`clap`, `rusqlite`, `ignore`, `rayon`, `xxhash-rust`, `serde`, `serde_json`,
+`anyhow`, `regex`. None is copyleft — commercial use and closed-source
+distribution are fine. The only obligation is to ship each crate's copyright
+notice and license text (e.g. a `THIRD_PARTY_NOTICES.md`).
+
+`universal-ctags` is GPL-licensed, but `rustytokens` invokes it only as an
+external program over `PATH` (subprocess + stdio, no linking, no bundling). That
+keeps it a separate program and does not impose GPL on `rustytokens` itself. Do
+not bundle the `ctags` binary into a distributed product — that is what would
+trigger GPL obligations for that binary. Keep it a user-installed prerequisite.
+
+Naming: `rustytokens` is distinct from `toktoken`. If this goes commercial,
+avoid "toktoken-compatible" or similar wording in marketing.
diff --git a/src/cli.rs b/src/cli.rs
new file mode 100644
index 0000000..64a7df5
--- /dev/null
+++ b/src/cli.rs
@@ -0,0 +1,107 @@
+//! clap definitions for all subcommands.
+
+use std::path::PathBuf;
+
+use clap::{Parser, Subcommand};
+
+#[derive(Parser)]
+#[command(
+    name = "rustytokens",
+    version,
+    about = "Native codebase indexer + MCP server"
+)]
+pub struct Cli {
+    /// Project root for index-backed commands (defaults to current directory)
+    #[arg(short, long, global = true, default_value = ".")]
+    pub project: PathBuf,
+
+    /// Output format: json or table
+    #[arg(long, global = true, default_value = "json")]
+    pub format: String,
+
+    /// Compact JSON output
+    #[arg(long, global = true)]
+    pub compact: bool,
+
+    #[command(subcommand)]
+    pub command: Command,
+}
+
+#[derive(Subcommand)]
+pub enum Command {
+    /// Build or refresh the index
+    Index {
+        #[command(subcommand)]
+        sub: IndexCommand,
+    },
+    /// Search symbols or file contents
+    Search {
+        #[command(subcommand)]
+        sub: SearchCommand,
+    },
+    /// Inspect symbols, files, outlines, the tree, or cycles
+    Inspect {
+        #[command(subcommand)]
+        sub: InspectCommand,
+    },
+    /// Find importers or dead code
+    Find {
+        #[command(subcommand)]
+        sub: FindCommand,
+    },
+    /// Start the MCP server over stdio
+    Serve,
+    /// Show index statistics
+    Stats,
+}
+
+#[derive(Subcommand)]
+pub enum IndexCommand {
+    /// Index a project from scratch
+    Create { path: PathBuf },
+    /// Re-index only changed files
+    Update { path: PathBuf },
+}
+
+#[derive(Subcommand)]
+pub enum SearchCommand {
+    /// Search symbols by name
+    Symbols { query: String },
+    /// Full-text search over file contents
+    Text { query: String },
+}
+
+#[derive(Subcommand)]
+pub enum InspectCommand {
+    /// Source code of a single symbol by id
+    Symbol { id: i64 },
+    /// Symbol outline of a file
+    Outline { file: String },
+    /// Read a file or a line range (e.g. --lines 10-40)
+    File {
+        file: String,
+        #[arg(long)]
+        lines: Option<String>,
+    },
+    /// Indexed file tree
+    Tree {
+        #[arg(long)]
+        depth: Option<usize>,
+    },
+    /// Files transitively affected by a change
+    BlastRadius {
+        file: String,
+        #[arg(long)]
+        depth: Option<usize>,
+    },
+    /// Find circular imports
+    Cycles,
+}
+
+#[derive(Subcommand)]
+pub enum FindCommand {
+    /// Who imports this file
+    Importers { file: String },
+    /// Files with no importers
+    Dead,
+}
diff --git a/src/config.rs b/src/config.rs
new file mode 100644
index 0000000..d840e37
--- /dev/null
+++ b/src/config.rs
@@ -0,0 +1,81 @@
+//! Project configuration: paths, cache dir, ignore patterns, language mapping.
+
+use std::collections::hash_map::DefaultHasher;
+use std::hash::{Hash, Hasher};
+use std::path::{Path, PathBuf};
+
+/// Directory names skipped during discovery (own list).
+pub const SKIP_DIRS: &[&str] = &[
+    ".git",
+    ".hg",
+    ".svn",
+    "node_modules",
+    "target",
+    "vendor",
+    "venv",
+    ".venv",
+    "__pycache__",
+    "dist",
+    "build",
+    ".idea",
+    ".vscode",
+    ".mypy_cache",
+    ".pytest_cache",
+    ".next",
+    ".nuxt",
+    "bower_components",
+    "coverage",
+    "out",
+];
+
+/// Map a file extension to a language label, or `None` if unsupported.
+pub fn language_for(path: &Path) -> Option<&'static str> {
+    let ext = path.extension()?.to_str()?;
+    Some(match ext {
+        "rs" => "rust",
+        "java" => "java",
+        "py" => "python",
+        "c" | "h" => "c",
+        "cc" | "cpp" | "cxx" | "hpp" | "hh" | "hxx" => "cpp",
+        "ts" | "tsx" | "mts" | "cts" => "typescript",
+        "js" | "jsx" | "mjs" | "cjs" => "javascript",
+        "html" | "htm" => "html",
+        "css" => "css",
+        _ => return None,
+    })
+}
+
+/// Base cache directory for index databases.
+pub fn cache_dir() -> PathBuf {
+    let base = std::env::var("XDG_CACHE_HOME")
+        .ok()
+        .filter(|s| !s.is_empty())
+        .map(PathBuf::from)
+        .or_else(|| {
+            std::env::var("HOME")
+                .ok()
+                .map(|h| PathBuf::from(h).join(".cache"))
+        })
+        .unwrap_or_else(|| PathBuf::from("."));
+    base.join("rustytokens")
+}
+
+/// Deterministic short key for a project path (used to name the cache DB).
+fn project_key(path: &str) -> String {
+    let mut h = DefaultHasher::new();
+    path.hash(&mut h);
+    format!("{:016x}", h.finish())
+}
+
+/// Path of the SQLite index DB for a project root.
+pub fn index_db_path(project: &Path) -> PathBuf {
+    let canon = project
+        .canonicalize()
+        .unwrap_or_else(|_| project.to_path_buf());
+    let key = project_key(&canon.to_string_lossy());
+    let name = project
+        .file_name()
+        .map(|n| n.to_string_lossy().into_owned())
+        .unwrap_or_else(|| "project".to_string());
+    cache_dir().join(format!("{name}-{key}.db"))
+}
diff --git a/src/ctags/mod.rs b/src/ctags/mod.rs
new file mode 100644
index 0000000..d48467c
--- /dev/null
+++ b/src/ctags/mod.rs
@@ -0,0 +1,65 @@
+//! Thin subprocess wrapper around universal-ctags (no linking, own structs).
+
+use std::io::Write;
+use std::path::Path;
+use std::process::{Command, Stdio};
+
+use anyhow::{Context, Result, anyhow};
+use serde::Deserialize;
+
+#[derive(Debug, Clone, Deserialize)]
+pub struct Tag {
+    pub name: String,
+    pub path: String,
+    #[serde(default)]
+    pub line: Option<u64>,
+    #[serde(default)]
+    pub end: Option<u64>,
+    #[serde(default)]
+    pub kind: Option<String>,
+    #[serde(default)]
+    pub scope: Option<String>,
+    #[serde(default)]
+    pub signature: Option<String>,
+}
+
+/// Run ctags over `files`, returning parsed JSON tags.
+pub fn run(files: &[&Path]) -> Result<Vec<Tag>> {
+    if files.is_empty() {
+        return Ok(Vec::new());
+    }
+    let mut child = Command::new("ctags")
+        .args(["--output-format=json", "--fields=+nKeSt", "-L", "-"])
+        .stdin(Stdio::piped())
+        .stdout(Stdio::piped())
+        .stderr(Stdio::piped())
+        .spawn()
+        .context("failed to start ctags (is universal-ctags installed?)")?;
+
+    {
+        let stdin = child
+            .stdin
+            .as_mut()
+            .ok_or_else(|| anyhow!("ctags stdin unavailable"))?;
+        for f in files {
+            writeln!(stdin, "{}", f.to_string_lossy())?;
+        }
+    }
+
+    let output = child.wait_with_output().context("ctags failed")?;
+    if !output.status.success() {
+        let err = String::from_utf8_lossy(&output.stderr);
+        return Err(anyhow!("ctags exited with {}: {}", output.status, err));
+    }
+
+    let mut tags = Vec::new();
+    for line in output.stdout.split(|b| *b == b'\n') {
+        if line.is_empty() {
+            continue;
+        }
+        if let Ok(t) = serde_json::from_slice::<Tag>(line) {
+            tags.push(t);
+        }
+    }
+    Ok(tags)
+}
diff --git a/src/discovery/mod.rs b/src/discovery/mod.rs
new file mode 100644
index 0000000..2f797c3
--- /dev/null
+++ b/src/discovery/mod.rs
@@ -0,0 +1,59 @@
+//! Filesystem walk with smart filtering, producing the list of source files to index.
+
+use std::path::{Path, PathBuf};
+
+use anyhow::Result;
+
+use crate::config::{SKIP_DIRS, language_for};
+
+#[derive(Debug, Clone)]
+pub struct SourceFile {
+    /// Absolute path on disk.
+    pub path: PathBuf,
+    /// Path relative to the project root (forward slashes).
+    pub rel: String,
+    pub language: &'static str,
+}
+
+pub fn discover(project: &Path) -> Result<Vec<SourceFile>> {
+    let project_abs = project
+        .canonicalize()
+        .unwrap_or_else(|_| project.to_path_buf());
+    let mut builder = ignore::WalkBuilder::new(&project_abs);
+    builder.standard_filters(true);
+    builder.require_git(false);
+    builder.filter_entry(|entry| {
+        if entry.file_type().is_some_and(|t| t.is_dir()) {
+            let name = entry.file_name().to_string_lossy();
+            !SKIP_DIRS.iter().any(|d| *d == name)
+        } else {
+            true
+        }
+    });
+
+    let mut out = Vec::new();
+    for entry in builder.build() {
+        let entry = match entry {
+            Ok(e) => e,
+            Err(_) => continue,
+        };
+        let path = entry.path();
+        if entry.file_type().is_some_and(|t| t.is_dir()) {
+            continue;
+        }
+        let Some(language) = language_for(path) else {
+            continue;
+        };
+        let rel = path
+            .strip_prefix(&project_abs)
+            .map(|p| p.to_string_lossy().replace('\\', "/"))
+            .unwrap_or_else(|_| path.to_string_lossy().replace('\\', "/"));
+        out.push(SourceFile {
+            path: path.to_path_buf(),
+            rel,
+            language,
+        });
+    }
+    out.sort_by(|a, b| a.rel.cmp(&b.rel));
+    Ok(out)
+}
diff --git a/src/graph/mod.rs b/src/graph/mod.rs
new file mode 100644
index 0000000..a7ea5de
--- /dev/null
+++ b/src/graph/mod.rs
@@ -0,0 +1,177 @@
+//! Import graph: cycles (Tarjan SCC), dead files, blast radius (BFS).
+
+use std::collections::{HashMap, VecDeque};
+
+use crate::index::store::ImportRow;
+
+pub struct Graph {
+    adj: HashMap<i64, Vec<i64>>, // from_file_id -> to_file_id
+    rev: HashMap<i64, Vec<i64>>, // to_file_id -> from_file_id
+}
+
+impl Graph {
+    pub fn from_imports(imports: &[ImportRow]) -> Self {
+        let mut adj: HashMap<i64, Vec<i64>> = HashMap::new();
+        let mut rev: HashMap<i64, Vec<i64>> = HashMap::new();
+        for imp in imports {
+            adj.entry(imp.from_file_id)
+                .or_default()
+                .push(imp.to_file_id);
+            rev.entry(imp.to_file_id)
+                .or_default()
+                .push(imp.from_file_id);
+        }
+        Graph { adj, rev }
+    }
+
+    /// Strongly-connected components with more than one node (or a self-loop).
+    pub fn cycles(&self) -> Vec<Vec<i64>> {
+        let mut sccs = tarjan_scc(&self.adj);
+        sccs.retain(|scc| {
+            scc.len() > 1
+                || (scc.len() == 1
+                    && self
+                        .adj
+                        .get(&scc[0])
+                        .map(|v| v.contains(&scc[0]))
+                        .unwrap_or(false))
+        });
+        for scc in &mut sccs {
+            scc.sort_unstable();
+        }
+        sccs
+    }
+
+    /// Files with no incoming import edges (nobody imports them).
+    pub fn dead_nodes(&self, all_file_ids: &[i64]) -> Vec<i64> {
+        let mut dead: Vec<i64> = all_file_ids
+            .iter()
+            .copied()
+            .filter(|id| self.rev.get(id).map(|v| v.is_empty()).unwrap_or(true))
+            .collect();
+        dead.sort_unstable();
+        dead
+    }
+
+    /// BFS over the reverse graph: which files (transitively) import `start`.
+    pub fn blast_radius(&self, start: i64, max_depth: usize) -> Vec<(i64, usize)> {
+        let mut out = Vec::new();
+        let mut seen = HashMap::new();
+        seen.insert(start, 0usize);
+        let mut queue = VecDeque::from([(start, 0usize)]);
+        while let Some((node, depth)) = queue.pop_front() {
+            if depth >= max_depth {
+                continue;
+            }
+            if let Some(parents) = self.rev.get(&node) {
+                for &p in parents {
+                    if let std::collections::hash_map::Entry::Vacant(e) = seen.entry(p) {
+                        e.insert(depth + 1);
+                        queue.push_back((p, depth + 1));
+                    }
+                }
+            }
+        }
+        for (id, d) in seen {
+            if id != start {
+                out.push((id, d));
+            }
+        }
+        out.sort_by_key(|(_, d)| *d);
+        out
+    }
+}
+
+/// Iterative Tarjan SCC. Returns strongly-connected components.
+fn tarjan_scc(adj: &HashMap<i64, Vec<i64>>) -> Vec<Vec<i64>> {
+    let mut index_counter = 0usize;
+    let mut indices: HashMap<i64, usize> = HashMap::new();
+    let mut lowlinks: HashMap<i64, usize> = HashMap::new();
+    let mut stack: Vec<i64> = Vec::new();
+    let mut on_stack: HashMap<i64, bool> = HashMap::new();
+    let mut sccs: Vec<Vec<i64>> = Vec::new();
+
+    let nodes: Vec<i64> = {
+        let mut set = std::collections::HashSet::new();
+        for (k, v) in adj {
+            set.insert(*k);
+            for t in v {
+                set.insert(*t);
+            }
+        }
+        let mut v: Vec<i64> = set.into_iter().collect();
+        v.sort_unstable();
+        v
+    };
+
+    #[allow(clippy::too_many_arguments)]
+    fn strongconnect(
+        v: i64,
+        adj: &HashMap<i64, Vec<i64>>,
+        index_counter: &mut usize,
+        indices: &mut HashMap<i64, usize>,
+        lowlinks: &mut HashMap<i64, usize>,
+        stack: &mut Vec<i64>,
+        on_stack: &mut HashMap<i64, bool>,
+        sccs: &mut Vec<Vec<i64>>,
+    ) {
+        indices.insert(v, *index_counter);
+        lowlinks.insert(v, *index_counter);
+        *index_counter += 1;
+        stack.push(v);
+        on_stack.insert(v, true);
+
+        if let Some(neighbors) = adj.get(&v) {
+            for &w in neighbors {
+                if !indices.contains_key(&w) {
+                    strongconnect(
+                        w,
+                        adj,
+                        index_counter,
+                        indices,
+                        lowlinks,
+                        stack,
+                        on_stack,
+                        sccs,
+                    );
+                    let lw = lowlinks[&w];
+                    let lv = lowlinks[&v];
+                    lowlinks.insert(v, lv.min(lw));
+                } else if on_stack.get(&w).copied().unwrap_or(false) {
+                    let iw = indices[&w];
+                    let lv = lowlinks[&v];
+                    lowlinks.insert(v, lv.min(iw));
+                }
+            }
+        }
+
+        if lowlinks[&v] == indices[&v] {
+            let mut component = Vec::new();
+            loop {
+                let w = stack.pop().unwrap();
+                on_stack.insert(w, false);
+                component.push(w);
+                if w == v {
+                    break;
+                }
+            }
+            sccs.push(component);
+        }
+    }
+
+    for &n in &nodes {
+        if !indices.contains_key(&n) {
+            strongconnect(
+                n,
+                adj,
+                &mut index_counter,
+                &mut indices,
+                &mut lowlinks,
+                &mut stack,
+                &mut on_stack,
+                &mut sccs,
+            );
+        }
+    }
+    sccs
+}
diff --git a/src/index/hashing.rs b/src/index/hashing.rs
new file mode 100644
index 0000000..ee1258b
--- /dev/null
+++ b/src/index/hashing.rs
@@ -0,0 +1,23 @@
+//! Content hashing for change detection.
+
+use std::fs::File;
+use std::io::Read;
+use std::path::Path;
+
+use anyhow::Result;
+
+pub fn hash_file(path: &Path) -> Result<String> {
+    let mut f = File::open(path)?;
+    let mut buf = Vec::new();
+    f.read_to_end(&mut buf)?;
+    Ok(format!("{:016x}", xxhash_rust::xxh3::xxh3_64(&buf)))
+}
+
+pub fn mtime_secs(path: &Path) -> i64 {
+    std::fs::metadata(path)
+        .and_then(|m| m.modified())
+        .ok()
+        .and_then(|t| t.duration_since(std::time::UNIX_EPOCH).ok())
+        .map(|d| d.as_secs() as i64)
+        .unwrap_or(0)
+}
diff --git a/src/index/imports.rs b/src/index/imports.rs
new file mode 100644
index 0000000..3eaa0d6
--- /dev/null
+++ b/src/index/imports.rs
@@ -0,0 +1,398 @@
+//! Import extraction (per-language) + best-effort resolution to file ids.
+
+use std::collections::HashMap;
+use std::sync::OnceLock;
+
+use regex::Regex;
+
+use crate::discovery::SourceFile;
+
+#[derive(Debug, Clone)]
+pub struct Import {
+    pub target: String,
+    pub import_type: String,
+    /// Directory levels a relative import ascends (Python `from ..x`).
+    pub levels: usize,
+}
+
+/// Extract import targets from a source file (own heuristic parsers).
+pub fn extract(f: &SourceFile) -> Vec<Import> {
+    let content = std::fs::read_to_string(&f.path).unwrap_or_default();
+    match f.language {
+        "python" => extract_python(&content),
+        "rust" => extract_rust(&content),
+        "typescript" | "javascript" => extract_ts(&content),
+        "c" | "cpp" => extract_c(&content),
+        "java" => extract_java(&content),
+        "html" => extract_html(&content),
+        _ => Vec::new(),
+    }
+}
+
+fn extract_python(content: &str) -> Vec<Import> {
+    let mut out = Vec::new();
+    for line in content.lines() {
+        let l = line.trim();
+        if let Some(rest) = l.strip_prefix("import ") {
+            for part in rest.split(',') {
+                let p = part.trim();
+                if !p.is_empty() {
+                    out.push(Import {
+                        target: p.to_string(),
+                        import_type: "import".into(),
+                        levels: 0,
+                    });
+                }
+            }
+        } else if let Some(rest) = l.strip_prefix("from ") {
+            // `from [..]<mod> import names` — leading dots = parent levels.
+            let module = rest.split_whitespace().next().unwrap_or("");
+            let dots = module.bytes().take_while(|b| *b == b'.').count();
+            let name = &module[dots..];
+            let levels = dots.saturating_sub(1);
+            if name.is_empty() {
+                // `from . import x` -> `x` lives `levels` dirs up.
+                let after = rest.split_once("import ").map(|(_, s)| s).unwrap_or("");
+                for n in after.split(',') {
+                    let n = n.trim().trim_end_matches('\\').trim();
+                    if !n.is_empty() {
+                        out.push(Import {
+                            target: n.to_string(),
+                            import_type: "from".into(),
+                            levels,
+                        });
+                    }
+                }
+            } else {
+                out.push(Import {
+                    target: name.to_string(),
+                    import_type: "from".into(),
+                    levels,
+                });
+            }
+        }
+    }
+    out
+}
+
+fn extract_rust(content: &str) -> Vec<Import> {
+    let mut out = Vec::new();
+    for line in content.lines() {
+        let l = line.trim();
+        if let Some(rest) = l.strip_prefix("use ") {
+            let rest = rest
+                .trim_end_matches(';')
+                .split('{')
+                .next()
+                .unwrap_or(rest)
+                .trim();
+            let path = rest
+                .trim_start_matches("crate::")
+                .trim_start_matches("self::")
+                .trim_start_matches("super::")
+                .trim_start_matches("::");
+            let mut segs: Vec<&str> = path.split("::").filter(|s| !s.is_empty()).collect();
+            if segs.is_empty() || matches!(segs[0], "std" | "core" | "alloc") {
+                continue;
+            }
+            // A trailing CamelCase segment is a type/symbol, not a module path.
+            if let Some(last) = segs.last()
+                && last.chars().next().is_some_and(char::is_uppercase)
+            {
+                segs.pop();
+            }
+            if let Some(first) = segs.first() {
+                out.push(Import {
+                    target: first.to_string(),
+                    import_type: "use".into(),
+                    levels: 0,
+                });
+            }
+            if segs.len() > 1 {
+                out.push(Import {
+                    target: segs.join("/"),
+                    import_type: "use".into(),
+                    levels: 0,
+                });
+            }
+        } else {
+            let mod_name = strip_mod_decl(l);
+            if let Some(name) = mod_name {
+                out.push(Import {
+                    target: name,
+                    import_type: "mod".into(),
+                    levels: 0,
+                });
+            }
+        }
+    }
+    out
+}
+
+/// Extract the module name from a `mod` declaration, handling visibility
+/// modifiers such as `pub`, `pub(crate)`, `pub(super)`, and attributes.
+fn strip_mod_decl(l: &str) -> Option<String> {
+    let mut rest = l;
+    // Strip leading attributes like `#[cfg(...)]`.
+    while rest.starts_with("#[") {
+        let end = rest.find("]\n").or_else(|| rest.find(']'))? + 1;
+        rest = rest[end..].trim_start();
+    }
+    if let Some(r) = rest.strip_prefix("pub ") {
+        rest = r;
+    } else if let Some(r) = rest.strip_prefix("pub(") {
+        let end = r.find(") ")? + 2;
+        rest = r[end..].trim_start();
+    }
+    let name = rest
+        .strip_prefix("mod ")?
+        .trim()
+        .trim_end_matches(';')
+        .trim();
+    if name.is_empty() || name.contains(' ') {
+        None
+    } else {
+        Some(name.to_string())
+    }
+}
+
+fn ts_import_re() -> &'static Regex {
+    static RE: OnceLock<Regex> = OnceLock::new();
+    RE.get_or_init(|| {
+        Regex::new(r#"(?:import|export)\s+(?:[^'"]*?from\s+)?['"]([^'"]+)['"]"#).unwrap()
+    })
+}
+
+fn ts_require_re() -> &'static Regex {
+    static RE: OnceLock<Regex> = OnceLock::new();
+    RE.get_or_init(|| Regex::new(r#"require\(\s*['"]([^'"]+)['"]\s*\)"#).unwrap())
+}
+
+fn extract_ts(content: &str) -> Vec<Import> {
+    let mut out = Vec::new();
+    for cap in ts_import_re().captures_iter(content) {
+        let target = cap[1].to_string();
+        let t = target.trim_start_matches("./");
+        out.push(Import {
+            target: t.to_string(),
+            import_type: "import".into(),
+            levels: 0,
+        });
+    }
+    for cap in ts_require_re().captures_iter(content) {
+        let target = cap[1].to_string();
+        let t = target.trim_start_matches("./");
+        out.push(Import {
+            target: t.to_string(),
+            import_type: "require".into(),
+            levels: 0,
+        });
+    }
+    out
+}
+
+fn extract_c(content: &str) -> Vec<Import> {
+    let mut out = Vec::new();
+    for line in content.lines() {
+        let l = line.trim();
+        if let Some(rest) = l.strip_prefix("#include") {
+            let inner = rest
+                .trim()
+                .trim_start_matches('"')
+                .trim_start_matches('<')
+                .split(['"', '>'])
+                .next()
+                .unwrap_or("");
+            if !inner.is_empty() {
+                out.push(Import {
+                    target: inner.to_string(),
+                    import_type: "include".into(),
+                    levels: 0,
+                });
+            }
+        }
+    }
+    out
+}
+
+fn extract_java(content: &str) -> Vec<Import> {
+    let mut out = Vec::new();
+    for line in content.lines() {
+        let l = line.trim();
+        if let Some(rest) = l.strip_prefix("import ") {
+            let rest = rest.trim_end_matches(';').trim_start_matches("static ");
+            let rest = rest.split_whitespace().next().unwrap_or(rest);
+            if !rest.is_empty() {
+                out.push(Import {
+                    target: rest.to_string(),
+                    import_type: "import".into(),
+                    levels: 0,
+                });
+            }
+        }
+    }
+    out
+}
+
+fn html_attr_re() -> &'static Regex {
+    static RE: OnceLock<Regex> = OnceLock::new();
+    RE.get_or_init(|| Regex::new(r#"(?:src|href)\s*=\s*["']([^"']+)["']"#).unwrap())
+}
+
+/// `<script src="...">` / `<link href="...">` as relative imports. ctags' HTML
+/// parser is weak, so symbol coverage here is best-effort.
+fn extract_html(content: &str) -> Vec<Import> {
+    html_attr_re()
+        .captures_iter(content)
+        .filter_map(|cap| {
+            let target = cap[1].trim();
+            // Skip absolute URLs, data URIs, and fragments.
+            if target.starts_with("http://")
+                || target.starts_with("https://")
+                || target.starts_with("//")
+                || target.starts_with("data:")
+                || target.starts_with('#')
+            {
+                return None;
+            }
+            let t = target.trim_start_matches("./");
+            if t.is_empty() {
+                return None;
+            }
+            Some(Import {
+                target: t.to_string(),
+                import_type: "asset".into(),
+                levels: 0,
+            })
+        })
+        .collect()
+}
+
+/// Best-effort mapping of an import target string to a file id.
+pub struct Resolver {
+    by_path: HashMap<String, i64>,
+    by_name: HashMap<String, i64>,
+    by_stem: HashMap<String, i64>,
+}
+
+/// Normalize an import target string (strip prefixes like `./`, `crate::`).
+fn clean(target: &str) -> Option<String> {
+    let t = target.trim();
+    if t.is_empty() {
+        return None;
+    }
+    let t = t.trim_start_matches("./");
+    let t = t
+        .trim_start_matches("crate::")
+        .trim_start_matches("self::")
+        .trim_start_matches("super::")
+        .trim_start_matches("::");
+    if t.is_empty() {
+        return None;
+    }
+    Some(t.to_string())
+}
+
+impl Resolver {
+    pub fn build(files: Vec<(String, i64)>) -> Self {
+        let mut by_path = HashMap::new();
+        let mut by_name = HashMap::new();
+        let mut by_stem = HashMap::new();
+        for (rel, id) in files {
+            by_path.insert(rel.clone(), id);
+            let name = rel.rsplit('/').next().unwrap_or(&rel).to_string();
+            by_name.entry(name.clone()).or_insert(id);
+            let stem = name
+                .rsplit_once('.')
+                .map(|(s, _)| s.to_string())
+                .unwrap_or(name);
+            by_stem.entry(stem).or_insert(id);
+        }
+        Resolver {
+            by_path,
+            by_name,
+            by_stem,
+        }
+    }
+
+    /// Resolve an import relative to the importing file's directory first,
+    /// ascending `levels` parent dirs for relative imports.
+    pub fn resolve_with_context(&self, target: &str, dir: &str, levels: usize) -> Option<i64> {
+        let t = clean(target)?;
+        let mut base = dir;
+        for _ in 0..levels {
+            base = base.rsplit_once('/').map(|(d, _)| d).unwrap_or("");
+        }
+        let base = if base.is_empty() {
+            String::new()
+        } else {
+            format!("{base}/")
+        };
+        self.resolve_relative(&base, &t)
+            .or_else(|| self.resolve_clean(&t))
+    }
+
+    fn resolve_clean(&self, t: &str) -> Option<i64> {
+        if let Some(id) = self.by_path.get(t) {
+            return Some(*id);
+        }
+        let slashed = t.replace('.', "/");
+        if slashed != t {
+            if let Some(id) = self.by_path.get(&slashed) {
+                return Some(*id);
+            }
+            if let Some(id) = self.try_module(&slashed) {
+                return Some(id);
+            }
+        }
+        if let Some(id) = self.try_module(t) {
+            return Some(id);
+        }
+        if let Some(id) = self.by_stem.get(t) {
+            return Some(*id);
+        }
+        let last = t.rsplit('/').next().unwrap_or(t);
+        if let Some(id) = self.by_stem.get(last) {
+            return Some(*id);
+        }
+        // Java dotted packages (`demo.Util`) — fall back to the final segment.
+        let last_dot = last.rsplit('.').next().unwrap_or(last);
+        if last_dot != last
+            && let Some(id) = self.by_stem.get(last_dot)
+        {
+            return Some(*id);
+        }
+        self.by_name.get(last).copied()
+    }
+
+    fn resolve_relative(&self, base: &str, t: &str) -> Option<i64> {
+        if let Some(id) = self.by_path.get(&format!("{base}{t}")) {
+            return Some(*id);
+        }
+        for ext in ["rs", "py", "ts", "tsx", "js", "cpp", "c", "h", "java"] {
+            if let Some(id) = self.by_path.get(&format!("{base}{t}.{ext}")) {
+                return Some(*id);
+            }
+        }
+        for entry in ["mod.rs", "__init__.py", "index.ts", "index.js", "index.tsx"] {
+            if let Some(id) = self.by_path.get(&format!("{base}{t}/{entry}")) {
+                return Some(*id);
+            }
+        }
+        None
+    }
+
+    fn try_module(&self, base: &str) -> Option<i64> {
+        for ext in ["rs", "py", "ts", "tsx", "js", "cpp", "c", "h", "java"] {
+            if let Some(id) = self.by_path.get(&format!("{base}.{ext}")) {
+                return Some(*id);
+            }
+        }
+        for entry in ["mod.rs", "__init__.py", "index.ts", "index.js", "index.tsx"] {
+            if let Some(id) = self.by_path.get(&format!("{base}/{entry}")) {
+                return Some(*id);
+            }
+        }
+        None
+    }
+}
diff --git a/src/index/mod.rs b/src/index/mod.rs
new file mode 100644
index 0000000..c4d794a
--- /dev/null
+++ b/src/index/mod.rs
@@ -0,0 +1,5 @@
+pub mod hashing;
+pub mod imports;
+pub mod pipeline;
+pub mod schema;
+pub mod store;
diff --git a/src/index/pipeline.rs b/src/index/pipeline.rs
new file mode 100644
index 0000000..4647efd
--- /dev/null
+++ b/src/index/pipeline.rs
@@ -0,0 +1,209 @@
+//! Index pipeline: hash, run ctags, extract imports, write to SQLite in one transaction.
+
+use std::collections::HashMap;
+use std::path::Path;
+
+use anyhow::{Context, Result};
+use rayon::prelude::*;
+use rusqlite::params;
+
+use crate::ctags;
+use crate::discovery::{self, SourceFile};
+use crate::index::{hashing, imports, store};
+
+#[derive(Debug, serde::Serialize)]
+pub struct IndexStats {
+    pub files: i64,
+    pub symbols: i64,
+    pub imports: i64,
+}
+
+/// (Re)index a project. `recreate` drops any existing index first.
+pub fn run(project: &Path, db_path: &Path, recreate: bool) -> Result<IndexStats> {
+    if recreate && db_path.exists() {
+        std::fs::remove_file(db_path).context("remove old index")?;
+    }
+    let conn = store::open(db_path)?;
+
+    let files = discovery::discover(project)?;
+
+    let existing: HashMap<String, (i64, String)> = store::all_files(&conn)?
+        .into_iter()
+        .map(|f| (f.path.clone(), (f.id, f.content_hash.clone())))
+        .collect();
+
+    // Hash all files in parallel.
+    let hashed: Vec<(String, String, i64, &'static str)> = files
+        .par_iter()
+        .map(|f| {
+            let h = hashing::hash_file(&f.path).unwrap_or_else(|_| "0000000000000000".to_string());
+            let m = hashing::mtime_secs(&f.path);
+            (f.rel.clone(), h, m, f.language)
+        })
+        .collect();
+
+    let by_rel: HashMap<&str, &SourceFile> = files.iter().map(|f| (f.rel.as_str(), f)).collect();
+    let abs_to_rel: HashMap<String, String> = files
+        .iter()
+        .map(|f| (f.path.to_string_lossy().into_owned(), f.rel.clone()))
+        .collect();
+
+    let changed: Vec<&SourceFile> = hashed
+        .iter()
+        .filter(|(rel, h, _, _)| existing.get(rel).map(|(_, oh)| oh != h).unwrap_or(true))
+        .filter_map(|(rel, ..)| by_rel.get(rel.as_str()).copied())
+        .collect();
+
+    let deleted_ids: Vec<i64> = existing
+        .iter()
+        .filter(|(rel, _)| !by_rel.contains_key(rel.as_str()))
+        .map(|(_, (id, _))| *id)
+        .collect();
+
+    conn.execute_batch("BEGIN;")?;
+
+    let mut file_ids: HashMap<String, i64> = HashMap::new();
+    for (rel, h, m, lang) in &hashed {
+        let id = store::upsert_file(&conn, rel, h, lang, *m)?;
+        file_ids.insert(rel.clone(), id);
+    }
+
+    for id in &deleted_ids {
+        store::delete_file(&conn, *id)?;
+        conn.execute("DELETE FROM content_fts WHERE rowid = ?1", [id])?;
+    }
+
+    // Run ctags once over changed files.
+    let changed_paths: Vec<&Path> = changed.iter().map(|f| f.path.as_path()).collect();
+    let tags = ctags::run(&changed_paths)?;
+    let mut tags_by_rel: HashMap<String, Vec<ctags::Tag>> = HashMap::new();
+    for t in tags {
+        if let Some(rel) = abs_to_rel.get(&t.path) {
+            tags_by_rel.entry(rel.clone()).or_default().push(t);
+        }
+    }
+
+    let resolver =
+        imports::Resolver::build(file_ids.iter().map(|(k, v)| (k.clone(), *v)).collect());
+
+    for f in &changed {
+        let fid = file_ids[&f.rel];
+        let content = std::fs::read_to_string(&f.path).unwrap_or_default();
+        let tags = tags_by_rel.get(&f.rel).cloned().unwrap_or_default();
+        store::replace_symbols(&conn, fid, &tags_to_symbols(&tags, &content))?;
+        store::clear_imports_for_file(&conn, fid)?;
+        let dir = f
+            .rel
+            .rsplit_once('/')
+            .map(|(d, _)| d)
+            .unwrap_or("")
+            .to_string();
+        for imp in imports::extract(f) {
+            if let Some(to) = resolver.resolve_with_context(&imp.target, &dir, imp.levels)
+                && to != fid
+            {
+                store::insert_import(&conn, fid, to, &imp.import_type)?;
+            }
+        }
+        conn.execute("DELETE FROM content_fts WHERE rowid = ?1", [fid])?;
+        conn.execute(
+            "INSERT INTO content_fts(rowid, path, content) VALUES (?1, ?2, ?3)",
+            params![fid, f.rel, content],
+        )?;
+    }
+
+    conn.execute_batch("COMMIT;")?;
+
+    let (files_n, symbols_n, imports_n) = store::stats(&conn)?;
+    Ok(IndexStats {
+        files: files_n,
+        symbols: symbols_n,
+        imports: imports_n,
+    })
+}
+
+fn tags_to_symbols(tags: &[ctags::Tag], content: &str) -> Vec<store::NewSymbol> {
+    let lines: Vec<&str> = content.lines().collect();
+    tags.iter()
+        .filter_map(|t| {
+            let line = t.line? as i64;
+            let end = t.end.map(|e| e as i64).unwrap_or(line);
+            let kind = t.kind.clone().unwrap_or_default();
+            let end = extend_block_end(&lines, line, end, &kind);
+            let name = t.name.clone();
+            let qualified_name = match &t.scope {
+                Some(s) if !name.starts_with(&format!("{s}.")) => format!("{s}.{name}"),
+                _ => name.clone(),
+            };
+            Some(store::NewSymbol {
+                name,
+                qualified_name,
+                kind,
+                signature: t.signature.clone(),
+                line_start: line,
+                line_end: end,
+            })
+        })
+        .collect()
+}
+
+/// ctags omits a body span for some kinds (e.g. Rust `fn`), leaving `end ==
+/// start` even for a multi-line block. Extend brace-based blocks to their
+/// closing brace so stored spans are correct for every reader.
+fn extend_block_end(lines: &[&str], start: i64, end: i64, kind: &str) -> i64 {
+    if !is_block_kind(kind) || end > start {
+        return end;
+    }
+    // Semicolon-terminated declarations (`mod foo;`, `struct Foo;`) have no body.
+    if let Some(line) = lines.get((start - 1) as usize)
+        && line.trim_end().ends_with(';')
+    {
+        return end;
+    }
+    let mut depth = 0i64;
+    let mut opened = false;
+    let mut out = end;
+    // ponytail: naive char brace count; braces in string/comment literals skew
+    // depth. Swap for a tokenizer only if real spans come back wrong.
+    for (i, line) in lines.iter().enumerate() {
+        let n = (i as i64) + 1;
+        if n < start {
+            continue;
+        }
+        for c in line.chars() {
+            match c {
+                '{' => {
+                    depth += 1;
+                    opened = true;
+                }
+                '}' => depth -= 1,
+                _ => {}
+            }
+        }
+        if opened {
+            out = n;
+        }
+        if opened && depth <= 0 {
+            break;
+        }
+    }
+    out
+}
+
+fn is_block_kind(kind: &str) -> bool {
+    matches!(
+        kind,
+        "function"
+            | "method"
+            | "struct"
+            | "class"
+            | "interface"
+            | "enum"
+            | "trait"
+            | "impl"
+            | "implementation"
+            | "module"
+            | "namespace"
+            | "union"
+    )
+}
diff --git a/src/index/schema.rs b/src/index/schema.rs
new file mode 100644
index 0000000..543d1eb
--- /dev/null
+++ b/src/index/schema.rs
@@ -0,0 +1,71 @@
+//! SQLite schema + minimal migration (schema_version in metadata).
+
+use anyhow::Result;
+use rusqlite::Connection;
+
+const SCHEMA_VERSION: i64 = 1;
+
+const SCHEMA: &str = r#"
+CREATE TABLE files (
+  id INTEGER PRIMARY KEY,
+  path TEXT NOT NULL UNIQUE,
+  content_hash TEXT NOT NULL,
+  language TEXT NOT NULL,
+  mtime INTEGER NOT NULL
+);
+CREATE TABLE symbols (
+  id INTEGER PRIMARY KEY,
+  file_id INTEGER NOT NULL REFERENCES files(id) ON DELETE CASCADE,
+  name TEXT NOT NULL,
+  qualified_name TEXT NOT NULL,
+  kind TEXT NOT NULL,
+  signature TEXT,
+  line_start INTEGER NOT NULL,
+  line_end INTEGER NOT NULL
+);
+CREATE INDEX idx_symbols_file ON symbols(file_id);
+CREATE INDEX idx_symbols_name ON symbols(name);
+CREATE TABLE imports (
+  id INTEGER PRIMARY KEY,
+  from_file_id INTEGER NOT NULL REFERENCES files(id) ON DELETE CASCADE,
+  to_file_id INTEGER NOT NULL REFERENCES files(id) ON DELETE CASCADE,
+  import_type TEXT NOT NULL
+);
+CREATE INDEX idx_imports_from ON imports(from_file_id);
+CREATE INDEX idx_imports_to ON imports(to_file_id);
+CREATE VIRTUAL TABLE symbols_fts USING fts5(
+  name, qualified_name, kind, signature,
+  content='symbols', content_rowid='id'
+);
+CREATE TRIGGER symbols_ai AFTER INSERT ON symbols BEGIN
+  INSERT INTO symbols_fts(rowid, name, qualified_name, kind, signature)
+  VALUES (new.id, new.name, new.qualified_name, new.kind, new.signature);
+END;
+CREATE TRIGGER symbols_ad AFTER DELETE ON symbols BEGIN
+  INSERT INTO symbols_fts(symbols_fts, rowid, name, qualified_name, kind, signature)
+  VALUES ('delete', old.id, old.name, old.qualified_name, old.kind, old.signature);
+END;
+CREATE VIRTUAL TABLE content_fts USING fts5(path UNINDEXED, content);
+"#;
+
+/// Create schema if missing, or migrate to the current version.
+pub fn init(conn: &mut Connection) -> Result<()> {
+    conn.execute_batch(
+        "CREATE TABLE IF NOT EXISTS metadata (key TEXT PRIMARY KEY, value TEXT NOT NULL);",
+    )?;
+    let version: i64 = conn
+        .query_row(
+            "SELECT COALESCE(CAST(value AS INTEGER), 0) FROM metadata WHERE key='schema_version'",
+            [],
+            |r| r.get(0),
+        )
+        .unwrap_or(0);
+    if version < SCHEMA_VERSION {
+        conn.execute_batch(SCHEMA)?;
+        conn.execute(
+            "INSERT OR REPLACE INTO metadata (key, value) VALUES ('schema_version', ?1)",
+            [SCHEMA_VERSION.to_string()],
+        )?;
+    }
+    Ok(())
+}
diff --git a/src/index/store.rs b/src/index/store.rs
new file mode 100644
index 0000000..2e4ecbb
--- /dev/null
+++ b/src/index/store.rs
@@ -0,0 +1,311 @@
+//! CRUD on files/symbols/imports.
+
+use std::path::Path;
+
+use anyhow::Result;
+use rusqlite::{Connection, OptionalExtension, params};
+
+use crate::index::schema;
+
+#[derive(Debug, Clone)]
+pub struct FileRow {
+    pub id: i64,
+    pub path: String,
+    pub content_hash: String,
+    pub language: String,
+}
+
+#[derive(Debug, Clone, serde::Serialize)]
+pub struct SymbolRow {
+    pub id: i64,
+    pub file_id: i64,
+    pub name: String,
+    pub qualified_name: String,
+    pub kind: String,
+    pub signature: Option<String>,
+    pub line_start: i64,
+    pub line_end: i64,
+}
+
+#[derive(Debug, Clone)]
+pub struct NewSymbol {
+    pub name: String,
+    pub qualified_name: String,
+    pub kind: String,
+    pub signature: Option<String>,
+    pub line_start: i64,
+    pub line_end: i64,
+}
+
+#[derive(Debug, Clone)]
+pub struct ImportRow {
+    pub from_file_id: i64,
+    pub to_file_id: i64,
+}
+
+/// Open (creating if needed) the index DB and apply schema.
+pub fn open(path: &Path) -> Result<Connection> {
+    if let Some(parent) = path.parent() {
+        std::fs::create_dir_all(parent)?;
+    }
+    let mut conn = Connection::open(path)?;
+    conn.execute_batch(
+        "PRAGMA journal_mode=WAL; PRAGMA foreign_keys=ON; PRAGMA synchronous=NORMAL;",
+    )?;
+    schema::init(&mut conn)?;
+    Ok(conn)
+}
+
+pub fn all_files(conn: &Connection) -> Result<Vec<FileRow>> {
+    let mut stmt = conn.prepare("SELECT id, path, content_hash, language FROM files")?;
+    let rows = stmt.query_map([], |r| {
+        Ok(FileRow {
+            id: r.get(0)?,
+            path: r.get(1)?,
+            content_hash: r.get(2)?,
+            language: r.get(3)?,
+        })
+    })?;
+    Ok(rows.collect::<std::result::Result<Vec<_>, _>>()?)
+}
+
+pub fn upsert_file(
+    conn: &Connection,
+    path: &str,
+    hash: &str,
+    language: &str,
+    mtime: i64,
+) -> Result<i64> {
+    conn.execute(
+        "INSERT INTO files (path, content_hash, language, mtime) VALUES (?1, ?2, ?3, ?4)
+         ON CONFLICT(path) DO UPDATE SET content_hash=?2, language=?3, mtime=?4",
+        params![path, hash, language, mtime],
+    )?;
+    // last_insert_rowid() is unreliable after an upsert that updates; query it.
+    Ok(conn.query_row("SELECT id FROM files WHERE path = ?1", [path], |r| r.get(0))?)
+}
+
+pub fn delete_file(conn: &Connection, id: i64) -> Result<()> {
+    conn.execute("DELETE FROM files WHERE id = ?1", [id])?;
+    Ok(())
+}
+
+pub fn file_by_id(conn: &Connection, id: i64) -> Result<Option<FileRow>> {
+    conn.query_row(
+        "SELECT id, path, content_hash, language FROM files WHERE id = ?1",
+        [id],
+        |r| {
+            Ok(FileRow {
+                id: r.get(0)?,
+                path: r.get(1)?,
+                content_hash: r.get(2)?,
+                language: r.get(3)?,
+            })
+        },
+    )
+    .optional()
+    .map_err(Into::into)
+}
+
+pub fn file_id_by_path(conn: &Connection, path: &str) -> Result<Option<i64>> {
+    Ok(conn
+        .query_row("SELECT id FROM files WHERE path = ?1", [path], |r| r.get(0))
+        .optional()?)
+}
+
+pub fn replace_symbols(conn: &Connection, file_id: i64, symbols: &[NewSymbol]) -> Result<()> {
+    conn.execute("DELETE FROM symbols WHERE file_id = ?1", [file_id])?;
+    let mut stmt = conn.prepare(
+        "INSERT INTO symbols (file_id, name, qualified_name, kind, signature, line_start, line_end)
+         VALUES (?1, ?2, ?3, ?4, ?5, ?6, ?7)",
+    )?;
+    for s in symbols {
+        stmt.execute(params![
+            file_id,
+            s.name,
+            s.qualified_name,
+            s.kind,
+            s.signature,
+            s.line_start,
+            s.line_end
+        ])?;
+    }
+    Ok(())
+}
+
+pub fn clear_imports_for_file(conn: &Connection, file_id: i64) -> Result<()> {
+    conn.execute("DELETE FROM imports WHERE from_file_id = ?1", [file_id])?;
+    Ok(())
+}
+
+pub fn insert_import(conn: &Connection, from: i64, to: i64, import_type: &str) -> Result<()> {
+    conn.execute(
+        "INSERT INTO imports (from_file_id, to_file_id, import_type) VALUES (?1, ?2, ?3)",
+        params![from, to, import_type],
+    )?;
+    Ok(())
+}
+
+pub fn all_imports(conn: &Connection) -> Result<Vec<ImportRow>> {
+    let mut stmt = conn.prepare("SELECT from_file_id, to_file_id FROM imports")?;
+    let rows = stmt.query_map([], |r| {
+        Ok(ImportRow {
+            from_file_id: r.get(0)?,
+            to_file_id: r.get(1)?,
+        })
+    })?;
+    Ok(rows.collect::<std::result::Result<Vec<_>, _>>()?)
+}
+
+pub fn symbol_by_id(conn: &Connection, id: i64) -> Result<Option<SymbolRow>> {
+    conn.query_row(
+        "SELECT id, file_id, name, qualified_name, kind, signature, line_start, line_end
+         FROM symbols WHERE id = ?1",
+        [id],
+        |r| {
+            Ok(SymbolRow {
+                id: r.get(0)?,
+                file_id: r.get(1)?,
+                name: r.get(2)?,
+                qualified_name: r.get(3)?,
+                kind: r.get(4)?,
+                signature: r.get(5)?,
+                line_start: r.get(6)?,
+                line_end: r.get(7)?,
+            })
+        },
+    )
+    .optional()
+    .map_err(Into::into)
+}
+
+pub fn symbols_for_file(conn: &Connection, file_id: i64) -> Result<Vec<SymbolRow>> {
+    let mut stmt = conn.prepare(
+        "SELECT id, file_id, name, qualified_name, kind, signature, line_start, line_end
+         FROM symbols WHERE file_id = ?1 ORDER BY line_start",
+    )?;
+    let rows = stmt.query_map([file_id], |r| {
+        Ok(SymbolRow {
+            id: r.get(0)?,
+            file_id: r.get(1)?,
+            name: r.get(2)?,
+            qualified_name: r.get(3)?,
+            kind: r.get(4)?,
+            signature: r.get(5)?,
+            line_start: r.get(6)?,
+            line_end: r.get(7)?,
+        })
+    })?;
+    Ok(rows.collect::<std::result::Result<Vec<_>, _>>()?)
+}
+
+pub fn importers_of(conn: &Connection, file_id: i64) -> Result<Vec<i64>> {
+    let mut stmt = conn.prepare("SELECT from_file_id FROM imports WHERE to_file_id = ?1")?;
+    let rows = stmt.query_map([file_id], |r| r.get(0))?;
+    Ok(rows.collect::<std::result::Result<Vec<_>, _>>()?)
+}
+
+/// Returns (files, symbols, imports) counts.
+pub fn stats(conn: &Connection) -> Result<(i64, i64, i64)> {
+    let files: i64 = conn.query_row("SELECT COUNT(*) FROM files", [], |r| r.get(0))?;
+    let symbols: i64 = conn.query_row("SELECT COUNT(*) FROM symbols", [], |r| r.get(0))?;
+    let imports: i64 = conn.query_row("SELECT COUNT(*) FROM imports", [], |r| r.get(0))?;
+    Ok((files, symbols, imports))
+}
+
+pub fn language_counts(conn: &Connection) -> Result<Vec<(String, i64)>> {
+    let mut stmt =
+        conn.prepare("SELECT language, COUNT(*) FROM files GROUP BY language ORDER BY 2 DESC")?;
+    let rows = stmt.query_map([], |r| Ok((r.get(0)?, r.get(1)?)))?;
+    Ok(rows.collect::<std::result::Result<Vec<_>, _>>()?)
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    fn mem() -> Connection {
+        let mut conn = Connection::open_in_memory().unwrap();
+        conn.execute_batch("PRAGMA foreign_keys=ON;").unwrap();
+        schema::init(&mut conn).unwrap();
+        conn
+    }
+
+    #[test]
+    fn file_insert_query_and_upsert() {
+        let conn = mem();
+        let id1 = upsert_file(&conn, "src/lib.rs", "hash1", "rust", 100).unwrap();
+        let id2 = upsert_file(&conn, "src/lib.rs", "hash2", "rust", 200).unwrap();
+        assert_eq!(id1, id2, "upsert reuses the same row");
+        let row = file_by_id(&conn, id1).unwrap().unwrap();
+        assert_eq!(row.content_hash, "hash2");
+        assert_eq!(row.language, "rust");
+        assert_eq!(all_files(&conn).unwrap().len(), 1);
+    }
+
+    #[test]
+    fn symbols_replace_and_query() {
+        let conn = mem();
+        let fid = upsert_file(&conn, "src/lib.rs", "h", "rust", 0).unwrap();
+        replace_symbols(
+            &conn,
+            fid,
+            &[
+                NewSymbol {
+                    name: "add".into(),
+                    qualified_name: "add".into(),
+                    kind: "function".into(),
+                    signature: Some("(a: i32, b: i32) -> i32".into()),
+                    line_start: 3,
+                    line_end: 5,
+                },
+                NewSymbol {
+                    name: "AuthService".into(),
+                    qualified_name: "AuthService".into(),
+                    kind: "struct".into(),
+                    signature: None,
+                    line_start: 7,
+                    line_end: 7,
+                },
+            ],
+        )
+        .unwrap();
+
+        let syms = symbols_for_file(&conn, fid).unwrap();
+        assert_eq!(syms.len(), 2);
+        assert_eq!(syms[0].name, "add");
+        assert_eq!(
+            symbol_by_id(&conn, syms[1].id).unwrap().unwrap().kind,
+            "struct"
+        );
+
+        // Replacing drops old symbols and re-inserts.
+        replace_symbols(
+            &conn,
+            fid,
+            &[NewSymbol {
+                name: "only".into(),
+                qualified_name: "only".into(),
+                kind: "function".into(),
+                signature: None,
+                line_start: 1,
+                line_end: 1,
+            }],
+        )
+        .unwrap();
+        assert_eq!(symbols_for_file(&conn, fid).unwrap().len(), 1);
+    }
+
+    #[test]
+    fn imports_roundtrip_and_importers() {
+        let conn = mem();
+        let a = upsert_file(&conn, "a.ts", "h", "typescript", 0).unwrap();
+        let b = upsert_file(&conn, "b.ts", "h", "typescript", 0).unwrap();
+        insert_import(&conn, a, b, "import").unwrap();
+        let imports = all_imports(&conn).unwrap();
+        assert_eq!(imports.len(), 1);
+        assert_eq!(imports[0].from_file_id, a);
+        assert_eq!(importers_of(&conn, b).unwrap(), vec![a]);
+        assert_eq!(stats(&conn).unwrap(), (2, 0, 1));
+    }
+}
diff --git a/src/main.rs b/src/main.rs
new file mode 100644
index 0000000..6875900
--- /dev/null
+++ b/src/main.rs
@@ -0,0 +1,81 @@
+mod cli;
+mod config;
+mod ctags;
+mod discovery;
+mod graph;
+mod index;
+mod mcp;
+mod ops;
+mod output;
+mod search;
+
+use anyhow::Result;
+use clap::Parser;
+use serde_json::Value;
+
+use cli::{Cli, Command, FindCommand, IndexCommand, InspectCommand, SearchCommand};
+
+fn main() {
+    if let Err(e) = run() {
+        if let Some(io) = e.downcast_ref::<std::io::Error>()
+            && io.kind() == std::io::ErrorKind::BrokenPipe
+        {
+            std::process::exit(0);
+        }
+        eprintln!("error: {e:#}");
+        std::process::exit(1);
+    }
+}
+
+fn run() -> Result<()> {
+    let cli = Cli::parse();
+    match &cli.command {
+        Command::Index { sub } => match sub {
+            IndexCommand::Create { path } => emit(&ops::index_create(path)?, &cli)?,
+            IndexCommand::Update { path } => emit(&ops::index_update(path)?, &cli)?,
+        },
+        Command::Search { sub } => match sub {
+            SearchCommand::Symbols { query } => {
+                emit(&ops::search_symbols(&cli.project, query)?, &cli)?
+            }
+            SearchCommand::Text { query } => emit(&ops::search_text(&cli.project, query)?, &cli)?,
+        },
+        Command::Inspect { sub } => match sub {
+            InspectCommand::Symbol { id } => emit(&ops::inspect_symbol(&cli.project, *id)?, &cli)?,
+            InspectCommand::Outline { file } => {
+                emit(&ops::inspect_outline(&cli.project, file)?, &cli)?
+            }
+            InspectCommand::File { file, lines } => emit(
+                &ops::inspect_file(&cli.project, file, lines.as_deref())?,
+                &cli,
+            )?,
+            InspectCommand::Tree { depth } => {
+                emit(&ops::inspect_tree(&cli.project, *depth)?, &cli)?
+            }
+            InspectCommand::BlastRadius { file, depth } => emit(
+                &ops::inspect_blast_radius(&cli.project, file, *depth)?,
+                &cli,
+            )?,
+            InspectCommand::Cycles => emit(&ops::inspect_cycles(&cli.project)?, &cli)?,
+        },
+        Command::Find { sub } => match sub {
+            FindCommand::Importers { file } => {
+                emit(&ops::find_importers(&cli.project, file)?, &cli)?
+            }
+            FindCommand::Dead => emit(&ops::find_dead(&cli.project)?, &cli)?,
+        },
+        Command::Serve => mcp::serve(&cli.project)?,
+        Command::Stats => emit(&ops::stats(&cli.project)?, &cli)?,
+    }
+    Ok(())
+}
+
+fn emit(value: &Value, cli: &Cli) -> Result<()> {
+    match cli.format.as_str() {
+        "table" => {
+            output::print_table(value);
+            Ok(())
+        }
+        _ => output::print_json(value, cli.compact),
+    }
+}
diff --git a/src/mcp/mod.rs b/src/mcp/mod.rs
new file mode 100644
index 0000000..a6e1e04
--- /dev/null
+++ b/src/mcp/mod.rs
@@ -0,0 +1,254 @@
+//! Minimal MCP server: JSON-RPC over stdio, dispatching to the same ops as the CLI.
+
+use std::io::{BufRead, Write};
+use std::path::Path;
+
+use anyhow::Result;
+use serde_json::{Value, json};
+
+const PROTOCOL_VERSION: &str = "2024-11-05";
+
+pub fn serve(project: &Path) -> Result<()> {
+    eprintln!("rustytokens MCP server listening on stdio");
+    let stdin = std::io::stdin();
+    let stdout = std::io::stdout();
+    for line in stdin.lock().lines() {
+        let line = match line {
+            Ok(l) => l,
+            Err(_) => break,
+        };
+        if line.trim().is_empty() {
+            continue;
+        }
+        let msg: Value = match serde_json::from_str(&line) {
+            Ok(m) => m,
+            Err(_) => continue,
+        };
+        if let Some(resp) = handle(&msg, project) {
+            let mut out = stdout.lock();
+            serde_json::to_writer(&mut out, &resp)?;
+            out.write_all(b"\n")?;
+            out.flush()?;
+        }
+    }
+    Ok(())
+}
+
+fn handle(msg: &Value, project: &Path) -> Option<Value> {
+    let method = msg.get("method")?.as_str()?;
+    let id = msg.get("id").cloned();
+
+    // Notifications have no id -> no response.
+    let id = id.as_ref()?;
+
+    match method {
+        "initialize" => Some(json!({
+            "jsonrpc": "2.0",
+            "id": id,
+            "result": {
+                "protocolVersion": PROTOCOL_VERSION,
+                "capabilities": { "tools": {} },
+                "serverInfo": { "name": "rustytokens", "version": env!("CARGO_PKG_VERSION") }
+            }
+        })),
+        "ping" => Some(json!({ "jsonrpc": "2.0", "id": id, "result": {} })),
+        "tools/list" => Some(json!({
+            "jsonrpc": "2.0",
+            "id": id,
+            "result": { "tools": tools() }
+        })),
+        "tools/call" => {
+            let params = msg.get("params").cloned().unwrap_or_else(|| json!({}));
+            let name = params.get("name").and_then(|n| n.as_str()).unwrap_or("");
+            let args = params
+                .get("arguments")
+                .cloned()
+                .unwrap_or_else(|| json!({}));
+            Some(json!({
+                "jsonrpc": "2.0",
+                "id": id,
+                "result": call_tool(name, &args, project)
+            }))
+        }
+        _ => Some(json!({
+            "jsonrpc": "2.0",
+            "id": id,
+            "error": { "code": -32601, "message": format!("method not found: {method}") }
+        })),
+    }
+}
+
+fn call_tool(name: &str, args: &Value, project: &Path) -> Value {
+    let result: Result<Value> = dispatch(name, args, project);
+    match result {
+        Ok(v) => json!({
+            "content": [{ "type": "text", "text": serde_json::to_string(&v).unwrap_or_default() }]
+        }),
+        Err(e) => json!({
+            "content": [{ "type": "text", "text": format!("error: {e:#}") }],
+            "isError": true
+        }),
+    }
+}
+
+fn dispatch(name: &str, args: &Value, project: &Path) -> Result<Value> {
+    use crate::ops;
+    let s = |k: &str| args.get(k).and_then(|v| v.as_str()).unwrap_or("");
+    match name {
+        "index_create" => ops::index_create(Path::new(s("path"))),
+        "index_update" => ops::index_update(Path::new(s("path"))),
+        "search_symbols" => ops::search_symbols(project, s("query")),
+        "search_text" => ops::search_text(project, s("query")),
+        "inspect_symbol" => ops::inspect_symbol(
+            project,
+            args.get("id").and_then(|v| v.as_i64()).unwrap_or(0),
+        ),
+        "inspect_outline" => ops::inspect_outline(project, s("file")),
+        "inspect_file" => ops::inspect_file(
+            project,
+            s("file"),
+            args.get("lines").and_then(|v| v.as_str()),
+        ),
+        "inspect_tree" => ops::inspect_tree(
+            project,
+            args.get("depth")
+                .and_then(|v| v.as_u64())
+                .map(|d| d as usize),
+        ),
+        "find_importers" => ops::find_importers(project, s("file")),
+        "find_dead" => ops::find_dead(project),
+        "inspect_cycles" => ops::inspect_cycles(project),
+        "inspect_blast_radius" => ops::inspect_blast_radius(
+            project,
+            s("file"),
+            args.get("depth")
+                .and_then(|v| v.as_u64())
+                .map(|d| d as usize),
+        ),
+        "stats" => ops::stats(project),
+        _ => anyhow::bail!("unknown tool: {name}"),
+    }
+}
+
+fn tools() -> Value {
+    json!([
+        tool(
+            "index_create",
+            "Index a project from scratch",
+            json!({
+                "type": "object",
+                "properties": { "path": { "type": "string", "description": "Project directory to index" } },
+                "required": ["path"]
+            })
+        ),
+        tool(
+            "index_update",
+            "Re-index only changed files",
+            json!({
+                "type": "object",
+                "properties": { "path": { "type": "string" } },
+                "required": ["path"]
+            })
+        ),
+        tool(
+            "search_symbols",
+            "Search symbols by name",
+            json!({
+                "type": "object",
+                "properties": { "query": { "type": "string" } },
+                "required": ["query"]
+            })
+        ),
+        tool(
+            "search_text",
+            "Full-text search over file contents",
+            json!({
+                "type": "object",
+                "properties": { "query": { "type": "string" } },
+                "required": ["query"]
+            })
+        ),
+        tool(
+            "inspect_symbol",
+            "Get the source code of a single symbol by id",
+            json!({
+                "type": "object",
+                "properties": { "id": { "type": "integer" } },
+                "required": ["id"]
+            })
+        ),
+        tool(
+            "inspect_outline",
+            "Get the symbol outline of a file",
+            json!({
+                "type": "object",
+                "properties": { "file": { "type": "string" } },
+                "required": ["file"]
+            })
+        ),
+        tool(
+            "inspect_file",
+            "Read a file or a line range",
+            json!({
+                "type": "object",
+                "properties": {
+                    "file": { "type": "string" },
+                    "lines": { "type": "string", "description": "Optional range, e.g. 10-40" }
+                },
+                "required": ["file"]
+            })
+        ),
+        tool(
+            "inspect_tree",
+            "Show the indexed file tree",
+            json!({
+                "type": "object",
+                "properties": { "depth": { "type": "integer" } }
+            })
+        ),
+        tool(
+            "find_importers",
+            "List files that import the given file",
+            json!({
+                "type": "object",
+                "properties": { "file": { "type": "string" } },
+                "required": ["file"]
+            })
+        ),
+        tool(
+            "find_dead",
+            "List files with no importers",
+            json!({ "type": "object" })
+        ),
+        tool(
+            "inspect_cycles",
+            "Find circular imports",
+            json!({ "type": "object" })
+        ),
+        tool(
+            "inspect_blast_radius",
+            "Files transitively affected by a change",
+            json!({
+                "type": "object",
+                "properties": {
+                    "file": { "type": "string" },
+                    "depth": { "type": "integer" }
+                },
+                "required": ["file"]
+            })
+        ),
+        tool(
+            "stats",
+            "Show index statistics",
+            json!({ "type": "object" })
+        ),
+    ])
+}
+
+fn tool(name: &str, description: &str, input_schema: Value) -> Value {
+    json!({
+        "name": name,
+        "description": description,
+        "inputSchema": input_schema
+    })
+}
diff --git a/src/ops.rs b/src/ops.rs
new file mode 100644
index 0000000..a4a788e
--- /dev/null
+++ b/src/ops.rs
@@ -0,0 +1,341 @@
+//! High-level operations shared by the CLI and the MCP server.
+
+use std::collections::BTreeMap;
+use std::path::Path;
+
+use anyhow::{Context, Result, bail};
+use rusqlite::Connection;
+use serde::Serialize;
+use serde_json::Value;
+
+use crate::config;
+use crate::graph::Graph;
+use crate::index::{pipeline, store};
+use crate::search;
+
+// ---- index ----
+
+pub fn index_create(project: &Path) -> Result<Value> {
+    let db = config::index_db_path(project);
+    let stats = pipeline::run(project, &db, true)?;
+    Ok(serde_json::to_value(stats)?)
+}
+
+pub fn index_update(project: &Path) -> Result<Value> {
+    let db = config::index_db_path(project);
+    let stats = pipeline::run(project, &db, false)?;
+    Ok(serde_json::to_value(stats)?)
+}
+
+// ---- search ----
+
+pub fn search_symbols(project: &Path, query: &str) -> Result<Value> {
+    let conn = open_read(project)?;
+    Ok(serde_json::to_value(search::search_symbols(&conn, query)?)?)
+}
+
+pub fn search_text(project: &Path, query: &str) -> Result<Value> {
+    let conn = open_read(project)?;
+    Ok(serde_json::to_value(search::search_text(&conn, query)?)?)
+}
+
+// ---- inspect ----
+
+pub fn inspect_symbol(project: &Path, id: i64) -> Result<Value> {
+    let conn = open_read(project)?;
+    let sym = store::symbol_by_id(&conn, id)?.with_context(|| format!("no symbol with id {id}"))?;
+    let file = store::file_by_id(&conn, sym.file_id)?
+        .with_context(|| format!("no file with id {}", sym.file_id))?;
+    let source = read_lines(project, &file.path, sym.line_start, sym.line_end)?;
+    Ok(serde_json::json!({
+        "id": sym.id,
+        "name": sym.name,
+        "qualified_name": sym.qualified_name,
+        "kind": sym.kind,
+        "signature": sym.signature,
+        "file": file.path,
+        "line_start": sym.line_start,
+        "line_end": sym.line_end,
+        "source": source,
+    }))
+}
+
+pub fn inspect_outline(project: &Path, file: &str) -> Result<Value> {
+    let conn = open_read(project)?;
+    let fid = file_id(&conn, file)?;
+    let symbols = store::symbols_for_file(&conn, fid)?;
+    Ok(serde_json::to_value(symbols)?)
+}
+
+pub fn inspect_file(project: &Path, file: &str, lines: Option<&str>) -> Result<Value> {
+    let conn = open_read(project)?;
+    let fid = file_id(&conn, file)?;
+    let frow = store::file_by_id(&conn, fid)?.unwrap();
+    let (start, end) = parse_range(lines);
+    let all = read_all_lines(project, &frow.path)?;
+    let total = all.len() as i64;
+    let (s, e) = (start.unwrap_or(1), end.unwrap_or(total));
+    let slice = all
+        .iter()
+        .enumerate()
+        .filter(|(i, _)| {
+            let n = (*i as i64) + 1;
+            n >= s && n <= e
+        })
+        .map(|(_, l)| l.clone())
+        .collect::<Vec<_>>()
+        .join("\n");
+    Ok(serde_json::json!({
+        "file": frow.path,
+        "language": frow.language,
+        "line_start": s,
+        "line_end": e.min(total),
+        "total_lines": total,
+        "content": slice,
+    }))
+}
+
+pub fn inspect_tree(project: &Path, depth: Option<usize>) -> Result<Value> {
+    let conn = open_read(project)?;
+    let files = store::all_files(&conn)?;
+    let paths: Vec<String> = files.into_iter().map(|f| f.path).collect();
+    let root_name = project
+        .file_name()
+        .map(|n| n.to_string_lossy().into_owned())
+        .unwrap_or_else(|| "project".to_string());
+    let tree = build_tree(&root_name, &paths, depth);
+    Ok(serde_json::to_value(tree)?)
+}
+
+// ---- find / graph ----
+
+pub fn find_importers(project: &Path, file: &str) -> Result<Value> {
+    let conn = open_read(project)?;
+    let fid = file_id(&conn, file)?;
+    let importers = store::importers_of(&conn, fid)?;
+    let paths = importers
+        .into_iter()
+        .map(|id| store::file_by_id(&conn, id).map(|f| f.map(|f| f.path)))
+        .collect::<std::result::Result<Vec<_>, _>>()?
+        .into_iter()
+        .flatten()
+        .collect::<Vec<_>>();
+    Ok(serde_json::to_value(paths)?)
+}
+
+pub fn find_dead(project: &Path) -> Result<Value> {
+    let conn = open_read(project)?;
+    let files = store::all_files(&conn)?;
+    let ids: Vec<i64> = files.iter().map(|f| f.id).collect();
+    let imports = store::all_imports(&conn)?;
+    let graph = Graph::from_imports(&imports);
+    let dead = graph.dead_nodes(&ids);
+    let out: Vec<Value> = dead
+        .into_iter()
+        .filter_map(|id| {
+            let f = files.iter().find(|f| f.id == id)?;
+            if is_entry_point(&f.path, &f.language) {
+                return None;
+            }
+            Some(serde_json::json!({"id": f.id, "path": f.path, "language": f.language}))
+        })
+        .collect();
+    Ok(serde_json::json!({"count": out.len(), "files": out}))
+}
+
+/// Entry-point files are legitimately never imported by anything else.
+fn is_entry_point(path: &str, language: &str) -> bool {
+    let name = path.rsplit('/').next().unwrap_or(path);
+    let stem = name.split('.').next().unwrap_or(name);
+    if matches!(stem, "main" | "lib") {
+        return true;
+    }
+    // Cargo compiles every file in these dirs as its own binary/crate.
+    if language == "rust" {
+        let top = path.split('/').next().unwrap_or(path);
+        if matches!(top, "tests" | "benches" | "examples") || path.starts_with("src/bin/") {
+            return true;
+        }
+    }
+    false
+}
+
+pub fn inspect_cycles(project: &Path) -> Result<Value> {
+    let conn = open_read(project)?;
+    let files = store::all_files(&conn)?;
+    let imports = store::all_imports(&conn)?;
+    let graph = Graph::from_imports(&imports);
+    let cycles = graph.cycles();
+    let path_of = |id: i64| {
+        files
+            .iter()
+            .find(|f| f.id == id)
+            .map(|f| f.path.clone())
+            .unwrap_or_else(|| format!("<id {id}>"))
+    };
+    let out: Vec<Vec<String>> = cycles
+        .into_iter()
+        .map(|c| c.into_iter().map(&path_of).collect())
+        .collect();
+    Ok(serde_json::json!({"count": out.len(), "cycles": out}))
+}
+
+pub fn inspect_blast_radius(project: &Path, file: &str, depth: Option<usize>) -> Result<Value> {
+    let conn = open_read(project)?;
+    let fid = file_id(&conn, file)?;
+    let files = store::all_files(&conn)?;
+    let imports = store::all_imports(&conn)?;
+    let graph = Graph::from_imports(&imports);
+    let max_depth = depth.unwrap_or(3);
+    let hits = graph.blast_radius(fid, max_depth);
+    let out: Vec<Value> = hits
+        .into_iter()
+        .filter_map(|(id, d)| {
+            files
+                .iter()
+                .find(|f| f.id == id)
+                .map(|f| serde_json::json!({"id": f.id, "path": f.path, "depth": d}))
+        })
+        .collect();
+    Ok(serde_json::json!({"file": file, "count": out.len(), "affected": out}))
+}
+
+// ---- stats ----
+
+pub fn stats(project: &Path) -> Result<Value> {
+    let conn = open_read(project)?;
+    let (files, symbols, imports) = store::stats(&conn)?;
+    let langs = store::language_counts(&conn)?;
+    Ok(serde_json::json!({
+        "files": files,
+        "symbols": symbols,
+        "imports": imports,
+        "languages": langs,
+    }))
+}
+
+// ---- helpers ----
+
+fn open_read(project: &Path) -> Result<Connection> {
+    let db = config::index_db_path(project);
+    if !db.exists() {
+        bail!(
+            "no index found for {}. Run `rustytokens index create <path>` first.",
+            project.display()
+        );
+    }
+    store::open(&db)
+}
+
+fn file_id(conn: &Connection, path: &str) -> Result<i64> {
+    store::file_id_by_path(conn, path)?.with_context(|| format!("file not indexed: {path}"))
+}
+
+fn read_lines(project: &Path, rel: &str, start: i64, end: i64) -> Result<String> {
+    let all = read_all_lines(project, rel)?;
+    Ok(all
+        .iter()
+        .enumerate()
+        .filter(|(i, _)| {
+            let n = (*i as i64) + 1;
+            n >= start && n <= end
+        })
+        .map(|(_, l)| l.clone())
+        .collect::<Vec<_>>()
+        .join("\n"))
+}
+
+fn read_all_lines(project: &Path, rel: &str) -> Result<Vec<String>> {
+    let path = project.join(rel);
+    let content = std::fs::read_to_string(&path)
+        .with_context(|| format!("cannot read {}", path.display()))?;
+    Ok(content.lines().map(|l| l.to_string()).collect())
+}
+
+fn parse_range(lines: Option<&str>) -> (Option<i64>, Option<i64>) {
+    let Some(s) = lines else { return (None, None) };
+    let parts: Vec<&str> = s.split('-').collect();
+    let start = parts.first().and_then(|p| p.trim().parse::<i64>().ok());
+    let end = parts.get(1).and_then(|p| p.trim().parse::<i64>().ok());
+    (start, end)
+}
+
+// ---- tree ----
+
+#[derive(Debug, Serialize)]
+struct TreeNode {
+    name: String,
+    path: String,
+    #[serde(rename = "type")]
+    kind: String,
+    #[serde(skip_serializing_if = "Vec::is_empty")]
+    children: Vec<TreeNode>,
+}
+
+#[derive(Default)]
+struct RawNode {
+    dirs: BTreeMap<String, RawNode>,
+    files: BTreeMap<String, String>,
+}
+
+fn build_tree(root_name: &str, paths: &[String], depth: Option<usize>) -> TreeNode {
+    let mut root = RawNode::default();
+    for p in paths {
+        let segs: Vec<&str> = p.split('/').collect();
+        insert_raw(&mut root, &segs, p);
+    }
+    let children = raw_to_nodes(&root, "", depth);
+    TreeNode {
+        name: root_name.to_string(),
+        path: String::new(),
+        kind: "dir".to_string(),
+        children,
+    }
+}
+
+fn insert_raw(node: &mut RawNode, segs: &[&str], full: &str) {
+    match segs {
+        [head] => {
+            node.files
+                .entry((*head).to_string())
+                .or_insert_with(|| full.to_string());
+        }
+        [head, rest @ ..] => {
+            let child = node.dirs.entry((*head).to_string()).or_default();
+            insert_raw(child, rest, full);
+        }
+        [] => {}
+    }
+}
+
+fn raw_to_nodes(node: &RawNode, base: &str, depth: Option<usize>) -> Vec<TreeNode> {
+    let mut out = Vec::new();
+    for (name, full) in &node.files {
+        out.push(TreeNode {
+            name: name.clone(),
+            path: full.clone(),
+            kind: "file".to_string(),
+            children: Vec::new(),
+        });
+    }
+    for (name, child) in &node.dirs {
+        let path = if base.is_empty() {
+            name.clone()
+        } else {
+            format!("{base}/{name}")
+        };
+        let expand = depth.map(|d| d > 0).unwrap_or(true);
+        let children = if expand {
+            raw_to_nodes(child, &path, depth.map(|d| d.saturating_sub(1)))
+        } else {
+            Vec::new()
+        };
+        out.push(TreeNode {
+            name: name.clone(),
+            path,
+            kind: "dir".to_string(),
+            children,
+        });
+    }
+    out
+}
diff --git a/src/output.rs b/src/output.rs
new file mode 100644
index 0000000..eff0914
--- /dev/null
+++ b/src/output.rs
@@ -0,0 +1,100 @@
+//! Output formatting: JSON (default) or a minimal table.
+
+use anyhow::Result;
+use serde::Serialize;
+use serde_json::Value;
+use std::io::Write;
+
+pub fn print_json<T: Serialize>(value: &T, compact: bool) -> Result<()> {
+    let mut buf = Vec::new();
+    if compact {
+        serde_json::to_writer(&mut buf, value)?;
+    } else {
+        serde_json::to_writer_pretty(&mut buf, value)?;
+    }
+    let mut out = std::io::stdout().lock();
+    out.write_all(&buf)?;
+    out.write_all(b"\n")?;
+    Ok(())
+}
+
+fn putline(s: &str) {
+    use std::io::Write;
+    let _ = writeln!(std::io::stdout().lock(), "{s}");
+}
+
+/// Minimal table renderer for array-of-objects and plain objects.
+pub fn print_table(value: &Value) {
+    match value {
+        Value::Array(items) if !items.is_empty() && items.iter().all(|i| i.is_object()) => {
+            let cols = collect_columns(items);
+            let mut rows = vec![cols.clone()];
+            for item in items {
+                let obj = item.as_object().unwrap();
+                rows.push(cols.iter().map(|c| cell_string(obj.get(c))).collect());
+            }
+            print_grid(&rows);
+        }
+        Value::Object(obj) => {
+            let mut rows = vec![vec!["key".to_string(), "value".to_string()]];
+            for (k, v) in obj {
+                rows.push(vec![k.clone(), cell_string(Some(v))]);
+            }
+            print_grid(&rows);
+        }
+        Value::Array(items) => {
+            for i in items {
+                putline(&cell_string(Some(i)));
+            }
+        }
+        other => putline(&cell_string(Some(other))),
+    }
+}
+
+fn collect_columns(items: &[Value]) -> Vec<String> {
+    let mut cols: Vec<String> = Vec::new();
+    for item in items {
+        if let Some(obj) = item.as_object() {
+            for k in obj.keys() {
+                if !cols.contains(k) {
+                    cols.push(k.clone());
+                }
+            }
+        }
+    }
+    cols
+}
+
+fn cell_string(v: Option<&Value>) -> String {
+    match v {
+        None | Some(Value::Null) => String::new(),
+        Some(Value::String(s)) => s.clone(),
+        Some(other) => serde_json::to_string(other).unwrap_or_default(),
+    }
+}
+
+fn print_grid(rows: &[Vec<String>]) {
+    let n = rows.iter().map(|r| r.len()).max().unwrap_or(0);
+    let mut widths = vec![0usize; n];
+    for r in rows {
+        for (i, c) in r.iter().enumerate() {
+            widths[i] = widths[i].max(c.chars().count());
+        }
+    }
+    for (ri, r) in rows.iter().enumerate() {
+        let mut line = String::new();
+        for (i, w) in widths.iter().enumerate() {
+            let c = r.get(i).cloned().unwrap_or_default();
+            line.push_str(&c);
+            if i + 1 < n {
+                line.push_str(&" ".repeat(w.saturating_sub(c.chars().count())));
+                line.push_str("  ");
+            }
+        }
+        putline(line.trim_end());
+        if ri == 0 {
+            let sep: Vec<String> = widths.iter().map(|w| "-".repeat(*w)).collect();
+            putline(sep.join("  ").trim_end());
+        }
+    }
+}
diff --git a/src/search/mod.rs b/src/search/mod.rs
new file mode 100644
index 0000000..d389f1f
--- /dev/null
+++ b/src/search/mod.rs
@@ -0,0 +1,130 @@
+//! FTS5-backed search with a simple own ranking (exact > prefix > fulltext).
+
+use std::collections::HashSet;
+
+use anyhow::Result;
+use rusqlite::{Connection, params};
+use serde::Serialize;
+
+#[derive(Debug, Serialize)]
+pub struct SymbolHit {
+    pub id: i64,
+    pub name: String,
+    pub qualified_name: String,
+    pub kind: String,
+    #[serde(skip_serializing_if = "Option::is_none")]
+    pub signature: Option<String>,
+    pub file: String,
+    pub line_start: i64,
+    pub line_end: i64,
+    pub match_type: String,
+}
+
+#[derive(Debug, Serialize)]
+pub struct TextHit {
+    pub file: String,
+    pub snippet: String,
+}
+
+const SYMBOL_COLS: &str =
+    "s.id, s.name, s.qualified_name, s.kind, s.signature, f.path, s.line_start, s.line_end";
+
+pub fn search_symbols(conn: &Connection, query: &str) -> Result<Vec<SymbolHit>> {
+    let q = query.trim();
+    let mut seen: HashSet<i64> = HashSet::new();
+    let mut out: Vec<SymbolHit> = Vec::new();
+    if q.is_empty() {
+        return Ok(out);
+    }
+
+    // 1) exact name (case-insensitive)
+    {
+        let mut stmt = conn.prepare(&format!(
+            "SELECT {SYMBOL_COLS} FROM symbols s JOIN files f ON f.id = s.file_id \
+             WHERE s.name = ?1 COLLATE NOCASE ORDER BY s.id LIMIT 200"
+        ))?;
+        let rows = stmt.query_map(params![q], |r| row_to_hit(r, "exact"))?;
+        push_hits(&mut out, &mut seen, rows)?;
+    }
+
+    // 2) prefix
+    {
+        let pat = format!("{}%", q);
+        let mut stmt = conn.prepare(&format!(
+            "SELECT {SYMBOL_COLS} FROM symbols s JOIN files f ON f.id = s.file_id \
+             WHERE s.name LIKE ?1 COLLATE NOCASE ORDER BY s.id LIMIT 200"
+        ))?;
+        let rows = stmt.query_map(params![pat], |r| row_to_hit(r, "prefix"))?;
+        push_hits(&mut out, &mut seen, rows)?;
+    }
+
+    // 3) fulltext over name/qualified_name/kind/signature
+    {
+        let phrase = fts_phrase(q);
+        let mut stmt = conn.prepare(&format!(
+            "SELECT {SYMBOL_COLS} FROM symbols_fts \
+             JOIN symbols s ON s.id = symbols_fts.rowid \
+             JOIN files f ON f.id = s.file_id \
+             WHERE symbols_fts MATCH ?1 ORDER BY rank LIMIT 200"
+        ))?;
+        let rows = stmt.query_map(params![phrase], |r| row_to_hit(r, "fulltext"))?;
+        push_hits(&mut out, &mut seen, rows)?;
+    }
+
+    Ok(out)
+}
+
+pub fn search_text(conn: &Connection, query: &str) -> Result<Vec<TextHit>> {
+    let q = query.trim();
+    if q.is_empty() {
+        return Ok(Vec::new());
+    }
+    let phrase = fts_phrase(q);
+    let mut stmt = conn.prepare(
+        "SELECT path, snippet(content_fts, 1, '«', '»', '…', 24) \
+         FROM content_fts WHERE content_fts MATCH ?1 ORDER BY rank LIMIT 100",
+    )?;
+    let rows = stmt.query_map(params![phrase], |r| {
+        Ok(TextHit {
+            file: r.get(0)?,
+            snippet: r.get(1)?,
+        })
+    })?;
+    Ok(rows.collect::<std::result::Result<Vec<_>, _>>()?)
+}
+
+fn row_to_hit(
+    r: &rusqlite::Row<'_>,
+    match_type: &str,
+) -> std::result::Result<SymbolHit, rusqlite::Error> {
+    Ok(SymbolHit {
+        id: r.get(0)?,
+        name: r.get(1)?,
+        qualified_name: r.get(2)?,
+        kind: r.get(3)?,
+        signature: r.get(4)?,
+        file: r.get(5)?,
+        line_start: r.get(6)?,
+        line_end: r.get(7)?,
+        match_type: match_type.to_string(),
+    })
+}
+
+fn push_hits(
+    out: &mut Vec<SymbolHit>,
+    seen: &mut HashSet<i64>,
+    rows: impl Iterator<Item = std::result::Result<SymbolHit, rusqlite::Error>>,
+) -> Result<()> {
+    for r in rows {
+        let hit = r?;
+        if seen.insert(hit.id) {
+            out.push(hit);
+        }
+    }
+    Ok(())
+}
+
+/// Wrap a user query as a safe FTS5 phrase.
+fn fts_phrase(q: &str) -> String {
+    format!("\"{}\"", q.replace('"', "\"\""))
+}
diff --git a/tests/cli.rs b/tests/cli.rs
new file mode 100644
index 0000000..31968c4
--- /dev/null
+++ b/tests/cli.rs
@@ -0,0 +1,480 @@
+//! End-to-end CLI tests against small, self-created fixture repos.
+
+use std::io::Write;
+use std::path::{Path, PathBuf};
+use std::process::{Command, Stdio};
+use std::sync::OnceLock;
+
+use serde_json::Value;
+
+fn bin() -> &'static str {
+    env!("CARGO_BIN_EXE_rustytokens")
+}
+
+/// Shared temp cache dir so tests never touch the real ~/.cache/rustytokens.
+fn cache_dir() -> &'static Path {
+    static DIR: OnceLock<PathBuf> = OnceLock::new();
+    DIR.get_or_init(|| {
+        let d = std::env::temp_dir().join(format!("rustytokens-test-cache-{}", std::process::id()));
+        std::fs::create_dir_all(&d).unwrap();
+        d
+    })
+}
+
+fn fixture(name: &str) -> PathBuf {
+    Path::new(env!("CARGO_MANIFEST_DIR"))
+        .join("tests/fixtures")
+        .join(name)
+}
+
+fn copy_dir(src: &Path, dst: &Path) {
+    std::fs::create_dir_all(dst).unwrap();
+    for entry in std::fs::read_dir(src).unwrap() {
+        let entry = entry.unwrap();
+        let to = dst.join(entry.file_name());
+        if entry.path().is_dir() {
+            copy_dir(&entry.path(), &to);
+        } else {
+            std::fs::copy(entry.path(), &to).unwrap();
+        }
+    }
+}
+
+/// Run the binary with the fixture's cache dir, returning parsed stdout JSON.
+fn run_json(args: &[&str]) -> Value {
+    let out = Command::new(bin())
+        .args(args)
+        .env("XDG_CACHE_HOME", cache_dir())
+        .output()
+        .expect("run rustytokens");
+    assert!(
+        out.status.success(),
+        "command failed: {:?}\nstderr: {}",
+        args,
+        String::from_utf8_lossy(&out.stderr)
+    );
+    serde_json::from_slice(&out.stdout).expect("stdout is valid JSON")
+}
+
+#[test]
+fn rust_index_search_and_dead() {
+    let fx = fixture("rustdemo");
+    run_json(&["index", "create", fx.to_str().unwrap()]);
+
+    let hits = run_json(&[
+        "--project",
+        fx.to_str().unwrap(),
+        "search",
+        "symbols",
+        "add",
+    ]);
+    let hit = hits
+        .as_array()
+        .unwrap()
+        .iter()
+        .find(|v| v["name"] == "add")
+        .expect("search finds `add`");
+    assert_eq!(hit["kind"], "function");
+
+    // inspect symbol by id returns the exact source.
+    let id = hit["id"].as_i64().unwrap();
+    let sym = run_json(&[
+        "--project",
+        fx.to_str().unwrap(),
+        "inspect",
+        "symbol",
+        &id.to_string(),
+    ]);
+    assert!(
+        sym["source"].as_str().unwrap().contains("a + b"),
+        "source contains function body"
+    );
+
+    // dead.rs is flagged; entry points lib.rs/main.rs are not.
+    let dead = run_json(&["--project", fx.to_str().unwrap(), "find", "dead"]);
+    let paths: Vec<&str> = dead["files"]
+        .as_array()
+        .unwrap()
+        .iter()
+        .map(|f| f["path"].as_str().unwrap())
+        .collect();
+    assert!(paths.contains(&"src/dead.rs"), "dead.rs flagged");
+    assert!(!paths.contains(&"src/lib.rs"), "lib.rs is an entry point");
+    assert!(!paths.contains(&"src/main.rs"), "main.rs is an entry point");
+}
+
+#[test]
+fn inspect_blast_radius_finds_affected_files() {
+    let src = fixture("rustdemo");
+    let tmp = cache_dir().join("blast-rustdemo");
+    let _ = std::fs::remove_dir_all(&tmp);
+    copy_dir(&src, &tmp);
+    run_json(&["index", "create", tmp.to_str().unwrap()]);
+
+    let blast = run_json(&[
+        "--project",
+        tmp.to_str().unwrap(),
+        "inspect",
+        "blast-radius",
+        "src/util.rs",
+    ]);
+    assert_eq!(blast["count"], 1);
+    assert_eq!(blast["file"], "src/util.rs");
+    let affected: Vec<&str> = blast["affected"]
+        .as_array()
+        .unwrap()
+        .iter()
+        .map(|f| f["path"].as_str().unwrap())
+        .collect();
+    assert_eq!(affected, ["src/lib.rs"], "lib.rs imports util.rs");
+}
+
+#[test]
+fn python_import_resolution_and_dead() {
+    let fx = fixture("pydemo");
+    run_json(&["index", "create", fx.to_str().unwrap()]);
+
+    let importers = run_json(&[
+        "--project",
+        fx.to_str().unwrap(),
+        "find",
+        "importers",
+        "util.py",
+    ]);
+    let names: Vec<&str> = importers
+        .as_array()
+        .unwrap()
+        .iter()
+        .map(|v| v.as_str().unwrap())
+        .collect();
+    assert!(names.contains(&"main.py"), "main.py imports util.py");
+
+    let dead = run_json(&["--project", fx.to_str().unwrap(), "find", "dead"]);
+    let paths: Vec<&str> = dead["files"]
+        .as_array()
+        .unwrap()
+        .iter()
+        .map(|f| f["path"].as_str().unwrap())
+        .collect();
+    assert!(paths.contains(&"dead.py"), "dead.py flagged");
+    assert!(!paths.contains(&"util.py"), "util.py is imported");
+}
+
+#[test]
+fn typescript_cycle_detection() {
+    let fx = fixture("tsdemo");
+    run_json(&["index", "create", fx.to_str().unwrap()]);
+
+    let cycles = run_json(&["--project", fx.to_str().unwrap(), "inspect", "cycles"]);
+    assert_eq!(cycles["count"], 1, "one cycle");
+    let cycle = &cycles["cycles"][0];
+    let files: Vec<&str> = cycle
+        .as_array()
+        .unwrap()
+        .iter()
+        .map(|v| v.as_str().unwrap())
+        .collect();
+    assert!(
+        files.contains(&"a.ts") && files.contains(&"b.ts"),
+        "a↔b cycle"
+    );
+}
+
+#[test]
+fn java_symbols_and_import_resolution() {
+    let fx = fixture("javademo");
+    run_json(&["index", "create", fx.to_str().unwrap()]);
+
+    let hits = run_json(&[
+        "--project",
+        fx.to_str().unwrap(),
+        "search",
+        "symbols",
+        "helper",
+    ]);
+    let hit = hits
+        .as_array()
+        .unwrap()
+        .iter()
+        .find(|v| v["name"] == "helper")
+        .expect("search finds `helper`");
+    assert_eq!(hit["kind"], "method");
+
+    // ctags reports Java constructors as `method` with a full `end` span, so
+    // the multi-line `Main` constructor must carry line_end > line_start.
+    let ctor = run_json(&[
+        "--project",
+        fx.to_str().unwrap(),
+        "search",
+        "symbols",
+        "Main",
+    ]);
+    let ctor_hit = ctor
+        .as_array()
+        .unwrap()
+        .iter()
+        .find(|v| v["name"] == "Main" && v["kind"] == "method")
+        .expect("search finds `Main` constructor");
+    assert!(
+        ctor_hit["line_end"].as_i64().unwrap() > ctor_hit["line_start"].as_i64().unwrap(),
+        "multi-line constructor has an extended span"
+    );
+
+    let importers = run_json(&[
+        "--project",
+        fx.to_str().unwrap(),
+        "find",
+        "importers",
+        "Util.java",
+    ]);
+    let names: Vec<&str> = importers
+        .as_array()
+        .unwrap()
+        .iter()
+        .map(|v| v.as_str().unwrap())
+        .collect();
+    assert!(names.contains(&"Main.java"), "Main.java imports Util.java");
+}
+
+#[test]
+fn c_and_cpp_symbols_and_imports() {
+    let cdemo = fixture("cdemo");
+    run_json(&["index", "create", cdemo.to_str().unwrap()]);
+
+    let hits = run_json(&[
+        "--project",
+        cdemo.to_str().unwrap(),
+        "search",
+        "symbols",
+        "helper",
+    ]);
+    assert!(
+        hits.as_array()
+            .unwrap()
+            .iter()
+            .any(|v| v["name"] == "helper"),
+        "c demo indexes `helper`"
+    );
+
+    let importers = run_json(&[
+        "--project",
+        cdemo.to_str().unwrap(),
+        "find",
+        "importers",
+        "util.h",
+    ]);
+    let names: Vec<&str> = importers
+        .as_array()
+        .unwrap()
+        .iter()
+        .map(|v| v.as_str().unwrap())
+        .collect();
+    assert!(names.contains(&"main.c") && names.contains(&"util.c"));
+
+    let cppdemo = fixture("cppdemo");
+    run_json(&["index", "create", cppdemo.to_str().unwrap()]);
+
+    let hits = run_json(&[
+        "--project",
+        cppdemo.to_str().unwrap(),
+        "search",
+        "symbols",
+        "add",
+    ]);
+    assert!(
+        hits.as_array().unwrap().iter().any(|v| v["name"] == "add"),
+        "cpp demo indexes `add`"
+    );
+
+    // ctags reports C++ constructors/destructors as `function` with an `end`
+    // span; the multi-line `Math` ctor must carry line_end > line_start.
+    let ctor = run_json(&[
+        "--project",
+        cppdemo.to_str().unwrap(),
+        "search",
+        "symbols",
+        "Math",
+    ]);
+    let ctor_hit = ctor
+        .as_array()
+        .unwrap()
+        .iter()
+        .find(|v| v["name"] == "Math" && v["kind"] == "function")
+        .expect("search finds `Math` constructor");
+    assert_eq!(ctor_hit["kind"], "function");
+    assert!(
+        ctor_hit["line_end"].as_i64().unwrap() > ctor_hit["line_start"].as_i64().unwrap(),
+        "multi-line constructor has an extended span"
+    );
+
+    // Destructor is also `function` with a ctags-owned `end` span (name `~Math`).
+    let dtor_hit = ctor
+        .as_array()
+        .unwrap()
+        .iter()
+        .find(|v| v["name"] == "~Math" && v["kind"] == "function")
+        .expect("search finds `~Math` destructor");
+    assert!(
+        dtor_hit["line_end"].as_i64().unwrap() > dtor_hit["line_start"].as_i64().unwrap(),
+        "multi-line destructor has an extended span"
+    );
+
+    let importers = run_json(&[
+        "--project",
+        cppdemo.to_str().unwrap(),
+        "find",
+        "importers",
+        "math.hpp",
+    ]);
+    let names: Vec<&str> = importers
+        .as_array()
+        .unwrap()
+        .iter()
+        .map(|v| v.as_str().unwrap())
+        .collect();
+    assert!(
+        names.contains(&"main.cpp") && names.contains(&"math.cpp"),
+        "both cpp files include math.hpp"
+    );
+}
+
+#[test]
+fn html_assets_are_discovered_and_imported() {
+    let fx = fixture("htmldemo");
+    run_json(&["index", "create", fx.to_str().unwrap()]);
+
+    let importers = run_json(&[
+        "--project",
+        fx.to_str().unwrap(),
+        "find",
+        "importers",
+        "app.js",
+    ]);
+    let names: Vec<&str> = importers
+        .as_array()
+        .unwrap()
+        .iter()
+        .map(|v| v.as_str().unwrap())
+        .collect();
+    assert!(
+        names.contains(&"index.html"),
+        "index.html imports app.js via <script src>"
+    );
+
+    let css = run_json(&[
+        "--project",
+        fx.to_str().unwrap(),
+        "find",
+        "importers",
+        "style.css",
+    ]);
+    let names: Vec<&str> = css
+        .as_array()
+        .unwrap()
+        .iter()
+        .map(|v| v.as_str().unwrap())
+        .collect();
+    assert!(
+        names.contains(&"index.html"),
+        "index.html imports style.css via <link href>"
+    );
+}
+
+#[test]
+fn mcp_serve_handles_tool_call() {
+    let src = fixture("rustdemo");
+    let tmp = cache_dir().join("mcp-rustdemo");
+    let _ = std::fs::remove_dir_all(&tmp);
+    copy_dir(&src, &tmp);
+    run_json(&["index", "create", tmp.to_str().unwrap()]);
+
+    let mut child = Command::new(bin())
+        .args(["--project", tmp.to_str().unwrap(), "serve"])
+        .env("XDG_CACHE_HOME", cache_dir())
+        .stdin(Stdio::piped())
+        .stdout(Stdio::piped())
+        .stderr(Stdio::null())
+        .spawn()
+        .expect("spawn serve");
+
+    {
+        let mut stdin = child.stdin.take().unwrap();
+        writeln!(stdin, r#"{{"jsonrpc":"2.0","id":1,"method":"initialize"}}"#).unwrap();
+        writeln!(
+            stdin,
+            r#"{{"jsonrpc":"2.0","id":2,"method":"tools/call","params":{{"name":"search_symbols","arguments":{{"query":"add"}}}}}}"#
+        )
+        .unwrap();
+    } // drop stdin -> closes the pipe, server exits
+
+    let out = child.wait_with_output().unwrap();
+    assert!(out.status.success(), "serve exits cleanly");
+
+    let responses: Vec<Value> = String::from_utf8_lossy(&out.stdout)
+        .lines()
+        .filter_map(|l| serde_json::from_str(l).ok())
+        .collect();
+    let init = responses
+        .iter()
+        .find(|r| r["id"] == 1)
+        .expect("initialize response");
+    assert_eq!(init["result"]["serverInfo"]["name"], "rustytokens");
+
+    let call = responses
+        .iter()
+        .find(|r| r["id"] == 2)
+        .expect("tools/call response");
+    let text = call["result"]["content"][0]["text"].as_str().unwrap();
+    let hits: Value = serde_json::from_str(text).unwrap();
+    assert!(
+        hits.as_array().unwrap().iter().any(|h| h["name"] == "add"),
+        "search_symbols over MCP finds `add`"
+    );
+}
+
+#[test]
+fn index_update_reindexes_changed_files() {
+    let src = fixture("javademo");
+    let tmp = cache_dir().join("update-javademo");
+    let _ = std::fs::remove_dir_all(&tmp);
+    copy_dir(&src, &tmp);
+
+    run_json(&["index", "create", tmp.to_str().unwrap()]);
+
+    let before = run_json(&[
+        "--project",
+        tmp.to_str().unwrap(),
+        "search",
+        "symbols",
+        "brandNew",
+    ]);
+    assert!(
+        before.as_array().unwrap().is_empty(),
+        "new symbol absent before update"
+    );
+
+    let lib = tmp.join("BrandNew.java");
+    std::fs::write(
+        &lib,
+        "package demo;\n\npublic class BrandNew {\n    public static int brandNew() { return 7; }\n}\n",
+    )
+    .unwrap();
+
+    run_json(&["index", "update", tmp.to_str().unwrap()]);
+
+    let after = run_json(&[
+        "--project",
+        tmp.to_str().unwrap(),
+        "search",
+        "symbols",
+        "brandNew",
+    ]);
+    assert!(
+        after
+            .as_array()
+            .unwrap()
+            .iter()
+            .any(|h| h["name"] == "brandNew"),
+        "index update picks up the new symbol"
+    );
+}
diff --git a/tests/fixtures/cdemo/dead.c b/tests/fixtures/cdemo/dead.c
new file mode 100644
index 0000000..121d063
--- /dev/null
+++ b/tests/fixtures/cdemo/dead.c
@@ -0,0 +1 @@
+int c_dead(void) { return 0; }
diff --git a/tests/fixtures/cdemo/main.c b/tests/fixtures/cdemo/main.c
new file mode 100644
index 0000000..d78d062
--- /dev/null
+++ b/tests/fixtures/cdemo/main.c
@@ -0,0 +1,5 @@
+#include "util.h"
+
+int main(void) {
+    return helper();
+}
diff --git a/tests/fixtures/cdemo/util.c b/tests/fixtures/cdemo/util.c
new file mode 100644
index 0000000..38aafd8
--- /dev/null
+++ b/tests/fixtures/cdemo/util.c
@@ -0,0 +1,3 @@
+#include "util.h"
+
+int helper(void) { return 0; }
diff --git a/tests/fixtures/cdemo/util.h b/tests/fixtures/cdemo/util.h
new file mode 100644
index 0000000..7f6ec3d
--- /dev/null
+++ b/tests/fixtures/cdemo/util.h
@@ -0,0 +1 @@
+int helper(void);
diff --git a/tests/fixtures/cppdemo/main.cpp b/tests/fixtures/cppdemo/main.cpp
new file mode 100644
index 0000000..0df5de5
--- /dev/null
+++ b/tests/fixtures/cppdemo/main.cpp
@@ -0,0 +1,5 @@
+#include "math.hpp"
+
+int main() {
+    return Math::add(1, 2);
+}
diff --git a/tests/fixtures/cppdemo/math.cpp b/tests/fixtures/cppdemo/math.cpp
new file mode 100644
index 0000000..8b51e25
--- /dev/null
+++ b/tests/fixtures/cppdemo/math.cpp
@@ -0,0 +1,13 @@
+#include "math.hpp"
+
+Math::Math(int scale) : scale_(scale) {
+    scale_ = scale;
+}
+
+Math::~Math() {
+    scale_ = 0;
+}
+
+int Math::add(int a, int b) { return a + b; }
+
+int Math::scaled(int v) const { return v * scale_; }
diff --git a/tests/fixtures/cppdemo/math.hpp b/tests/fixtures/cppdemo/math.hpp
new file mode 100644
index 0000000..f1e36a4
--- /dev/null
+++ b/tests/fixtures/cppdemo/math.hpp
@@ -0,0 +1,11 @@
+#pragma once
+
+class Math {
+public:
+    Math(int scale);
+    ~Math();
+    static int add(int a, int b);
+    int scaled(int v) const;
+private:
+    int scale_;
+};
diff --git a/tests/fixtures/htmldemo/app.js b/tests/fixtures/htmldemo/app.js
new file mode 100644
index 0000000..d914c60
--- /dev/null
+++ b/tests/fixtures/htmldemo/app.js
@@ -0,0 +1 @@
+console.log("hi");
diff --git a/tests/fixtures/htmldemo/index.html b/tests/fixtures/htmldemo/index.html
new file mode 100644
index 0000000..4366888
--- /dev/null
+++ b/tests/fixtures/htmldemo/index.html
@@ -0,0 +1,10 @@
+<!DOCTYPE html>
+<html>
+<head>
+  <link rel="stylesheet" href="style.css">
+  <script src="app.js"></script>
+</head>
+<body>
+  <h1>Hello</h1>
+</body>
+</html>
diff --git a/tests/fixtures/htmldemo/style.css b/tests/fixtures/htmldemo/style.css
new file mode 100644
index 0000000..991912d
--- /dev/null
+++ b/tests/fixtures/htmldemo/style.css
@@ -0,0 +1 @@
+body { color: red; }
diff --git a/tests/fixtures/javademo/Dead.java b/tests/fixtures/javademo/Dead.java
new file mode 100644
index 0000000..48a6329
--- /dev/null
+++ b/tests/fixtures/javademo/Dead.java
@@ -0,0 +1,5 @@
+package demo;
+
+public class Dead {
+    public static void unused() {}
+}
diff --git a/tests/fixtures/javademo/Main.java b/tests/fixtures/javademo/Main.java
new file mode 100644
index 0000000..73ae77c
--- /dev/null
+++ b/tests/fixtures/javademo/Main.java
@@ -0,0 +1,15 @@
+package demo;
+
+import demo.Util;
+
+public class Main {
+    private final int seed;
+
+    public Main(int seed) {
+        this.seed = seed;
+    }
+
+    public static void main(String[] args) {
+        System.out.println(Util.helper());
+    }
+}
diff --git a/tests/fixtures/javademo/Util.java b/tests/fixtures/javademo/Util.java
new file mode 100644
index 0000000..656f099
--- /dev/null
+++ b/tests/fixtures/javademo/Util.java
@@ -0,0 +1,5 @@
+package demo;
+
+public class Util {
+    public static int helper() { return 42; }
+}
diff --git a/tests/fixtures/pydemo/dead.py b/tests/fixtures/pydemo/dead.py
new file mode 100644
index 0000000..9e7a5a9
--- /dev/null
+++ b/tests/fixtures/pydemo/dead.py
@@ -0,0 +1,2 @@
+def py_dead():
+    return 0
diff --git a/tests/fixtures/pydemo/main.py b/tests/fixtures/pydemo/main.py
new file mode 100644
index 0000000..bc851f8
--- /dev/null
+++ b/tests/fixtures/pydemo/main.py
@@ -0,0 +1,5 @@
+from util import helper
+
+
+def run():
+    return helper()
diff --git a/tests/fixtures/pydemo/util.py b/tests/fixtures/pydemo/util.py
new file mode 100644
index 0000000..4c8b581
--- /dev/null
+++ b/tests/fixtures/pydemo/util.py
@@ -0,0 +1,2 @@
+def helper():
+    return 1
diff --git a/tests/fixtures/rustdemo/src/dead.rs b/tests/fixtures/rustdemo/src/dead.rs
new file mode 100644
index 0000000..7c1e328
--- /dev/null
+++ b/tests/fixtures/rustdemo/src/dead.rs
@@ -0,0 +1 @@
+pub fn totally_dead() {}
diff --git a/tests/fixtures/rustdemo/src/lib.rs b/tests/fixtures/rustdemo/src/lib.rs
new file mode 100644
index 0000000..f3257c4
--- /dev/null
+++ b/tests/fixtures/rustdemo/src/lib.rs
@@ -0,0 +1,5 @@
+pub mod util;
+
+pub fn add(a: i32, b: i32) -> i32 {
+    a + b
+}
diff --git a/tests/fixtures/rustdemo/src/main.rs b/tests/fixtures/rustdemo/src/main.rs
new file mode 100644
index 0000000..07cc682
--- /dev/null
+++ b/tests/fixtures/rustdemo/src/main.rs
@@ -0,0 +1,5 @@
+use rustdemo::add;
+
+fn main() {
+    println!("{}", add(2, 3));
+}
diff --git a/tests/fixtures/rustdemo/src/util.rs b/tests/fixtures/rustdemo/src/util.rs
new file mode 100644
index 0000000..7d099f6
--- /dev/null
+++ b/tests/fixtures/rustdemo/src/util.rs
@@ -0,0 +1,3 @@
+pub fn helper() -> String {
+    "ok".to_string()
+}
diff --git a/tests/fixtures/tsdemo/a.ts b/tests/fixtures/tsdemo/a.ts
new file mode 100644
index 0000000..9896a79
--- /dev/null
+++ b/tests/fixtures/tsdemo/a.ts
@@ -0,0 +1,3 @@
+import { b } from "./b";
+
+export const a = 1;
diff --git a/tests/fixtures/tsdemo/b.ts b/tests/fixtures/tsdemo/b.ts
new file mode 100644
index 0000000..9847a66
--- /dev/null
+++ b/tests/fixtures/tsdemo/b.ts
@@ -0,0 +1,3 @@
+import { a } from "./a";
+
+export const b = a;