Fix six open issues: stale imports, MCP validation, import-graph gaps, dup importers, I/O errors, scope docs

- pipeline: re-resolve imports for every file on update (not just changed),
  so add/remove/rename of a target fixes unchanged importers; propagate hash
  and read errors instead of treating unreadable files as empty
- discovery: report unreadable walk entries to stderr instead of dropping them
- imports: strip `pub` visibility so `pub use` re-exports resolve; share
  extension/module-entry probe lists (adds cc,cxx,hpp,hh,hxx,mts,cts,jsx,mjs,cjs)
- store: DISTINCT + ORDER in importers_of to dedup repeated edges
- mcp: validate required tool args (explicit isError), emit JSON-RPC -32700
  parse errors and -32600 invalid-request instead of silently skipping
- README: document the 13-tool surface vs toktoken's 27 and known gaps
- tests: regression coverage for update re-resolution, pub-use re-exports,
  importer dedup, and MCP error reporting

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

src/discovery/mod.rs

@@ -32,10 +32,15 @@ pub fn discover(project: &Path) -> Result<Vec<SourceFile>> {
     });
 
     let mut out = Vec::new();
+    let mut skipped = Vec::new();
     for entry in builder.build() {
         let entry = match entry {
             Ok(e) => e,
-            Err(_) => continue,
+            Err(e) => {
+                // Report unreadable entries instead of dropping them silently.
+                skipped.push(e.to_string());
+                continue;
+            }
         };
         let path = entry.path();
         if entry.file_type().is_some_and(|t| t.is_dir()) {
@@ -54,6 +59,9 @@ pub fn discover(project: &Path) -> Result<Vec<SourceFile>> {
             language,
         });
     }
+    for s in &skipped {
+        eprintln!("rustytokens: skipped unreadable entry: {s}");
+    }
     out.sort_by(|a, b| a.rel.cmp(&b.rel));
     Ok(out)
 }