fix(resolution): stop "Resolving refs" wedge on theme-vendoring repos; add exclude config + index watchdogs (#999) (#1009)

Three fixes for a repo that commits a large JS/TS theme/SDK (Metronic under
static/, ~1,600 tracked files):

1. A SECOND "Resolving refs" quadratic that #915 didn't cover. #915 capped
   import-name collisions; this caps method-name collisions (init/update/render
   re-declared on every widget), which flow through matchMethodCall Strategy 3
   and findBestMatch instead. New AMBIGUOUS_NAME_CEILING (default 500, env
   CODEGRAPH_AMBIGUOUS_NAME_CEILING): above it the fuzzy strategies decline
   rather than score K candidates — no proximity score can pick the one true
   target among thousands anyway. Resolving drops from O(K^2) to linear in refs
   (e.g. 900-file synthetic: 28.7s -> 3.4s), edge counts unchanged, and the cap
   never fires on normal repos (max real method-collision ~40).

2. A new `exclude` array in codegraph.json keeps git-TRACKED paths out of the
   index, which .gitignore can't do (enumeration is `git ls-files`). Mirrors the
   existing includeIgnored plumbing across the git, sync, and non-git-walk
   paths.

3. `index`/`init` now install the #850 liveness + #277 ppid watchdogs (which
   were serve-only), so a wedged or orphaned indexer self-terminates instead of
   pinning a core. The --liftoff-only relaunch's spawnSync can't forward
   signals, so killing the parent shim used to orphan the worker.

Tests: ubiquitous-name ceiling, exclude (incl. tracked-file exclusion on git +
non-git), orphan self-termination (POSIX), and ppid-parser units. Shared the
ppid parsers out of mcp/index.ts into mcp/ppid-watchdog.ts.

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

CHANGELOG.md

@@ -11,12 +11,15 @@ and adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ### New Features
 
+- You can now exclude committed directories from the index with an `exclude` list in `codegraph.json` — even when they're git-tracked. `.gitignore` can't drop a directory git already tracks, so a vendored theme or SDK that's checked into your repo (a committed Metronic theme under `static/`, a bundled vendor library) had no supported way to be kept out — it just bloated the graph and slowed indexing. Add a root `codegraph.json` with, e.g., `{ "exclude": ["static/", "**/vendor/**"] }` and those paths are skipped on indexing, sync, and file-watching, on both git and non-git projects. Patterns are gitignore-style and matched against repo-root-relative paths. This complements the existing `includeIgnored` (its opposite — opt *in* to gitignored embedded repos). (#999)
 - CodeGraph now follows C/C++ commands that are dispatched through macro-built function-pointer tables, so the handler functions they reach are no longer dead-ends in the graph. Many C projects register a handler into a struct's function-pointer field through a macro and a generated table — redis is the classic case: every command (`getCommand`, `decrbyCommand`, …) is wired into the command struct's `proc` field by a `MAKE_CMD(…)` table that lives in a generated, `#include`-d file, then invoked as `c->cmd->proc(c)`. CodeGraph now reads those macro-built tables — including ones whose struct type is itself a macro alias, whose table sits in an `#include`-d file that is never indexed on its own, or that are wrapped in conditional compilation (`#ifdef`) and defined inline with the struct. It recognizes function-pointer fields declared through a function typedef, and follows the receiver — a chained access (`c->cmd->proc`) or an array subscript through a file-scope table (`(cmdnames[i].cmd_func)(…)`) — across field types. It also follows dispatch through a bare array of function pointers with no struct wrapper at all — the opcode/handler-table pattern common in interpreters and emulators, where a table like `opcodes[op](…)` invokes one of many registered handler functions by index — linking the dispatcher to every handler in the array. The upshot: asking for the callers or blast radius of a command handler now finds the dispatcher that reaches it. For redis, `call` shows up as a caller of every command; for SQLite, the builtin SQL functions registered through `FUNCTION(...)` link to where they're invoked; for Vim, every `:ex` and normal-mode command links from the dispatcher. (#991, extending #932)
 - CodeGraph no longer times out when many agents query it at once. The shared background server that serves all your editor and agent sessions used to run every query on a single thread, so a burst of concurrent requests — for example a swarm of subagents exploring a large monorepo together — queued up behind one another and, while the heavy ones ran, froze the connection so finished answers couldn't even be sent back until the whole batch drained. Past a handful of simultaneous callers that routinely surfaced as MCP request timeouts. The shared server now answers queries across a pool of worker threads, so concurrent requests run in parallel and the connection stays responsive the whole time; when it's genuinely saturated a call returns a brief "busy, retry shortly" note (not an error) instead of hanging past your client's timeout. The pool sizes itself to your machine — roughly one worker per core, leaving one for coordination — and a single editor session is unaffected (no pool, no overhead). Set `CODEGRAPH_QUERY_POOL_SIZE` to choose a specific number of workers, or `0` to revert to single-threaded in-process queries.
 - When CodeGraph's MCP server runs with no default project of its own — started outside any repository (for example behind an MCP gateway), or at a monorepo root whose indexes live in sub-projects — it now marks `projectPath` as a required argument on every tool call. Before, `projectPath` was always optional, so an agent talking to such a server would often omit it, get back guidance to pass it, and not reliably retry — you had to nudge it by hand every time. Now the requirement is part of the tool definition the agent sees, so it supplies the path to the project it's working on the first time. When the server does have a default project — the normal case, launched inside your repo — `projectPath` stays optional and a call without it falls back to that project exactly as before. Thanks @wauxhall for the report. (#993)
 
 ### Fixes
 
+- A `codegraph index` or `codegraph init` that gets orphaned or wedged now stops itself instead of pinning a CPU core forever. If you killed the command (or the terminal/agent that launched it), the underlying indexer process used to keep running in the background — the parent couldn't pass the signal along — and a genuinely stuck index had nothing watching it either, since the self-recovery watchdogs were wired only into the background MCP server. Both gaps are closed: indexing now self-terminates when its parent goes away, and a main thread that stops making progress is killed so it can't hang indefinitely. Opt out with `CODEGRAPH_NO_WATCHDOG=1` (liveness) or `CODEGRAPH_PPID_POLL_MS=0` (orphan detection), matching the server. (#999)
+- Indexing no longer hangs at "Resolving refs" on a repo that commits a large JavaScript/TypeScript theme or SDK. A vendored admin theme (Metronic is the classic case — ~1,300 committed `.js` files) re-declares the same method names (`init`, `update`, `render`, `destroy`, …) on hundreds of widgets, and resolution used to score *every* same-named definition against *every* call — work that grows with the square of how many times a name repeats. On such a repo it pinned a CPU core for 15–30 minutes and effectively never finished. Resolution now declines to guess when a name is defined more times than any real codebase ever repeats one (the cutoff is generous — normal projects top out far below it and are completely unaffected), since no proximity heuristic can pick the one true target among thousands anyway. Indexing that previously wedged now completes in seconds, and precise resolution (imports, qualified names, class-name matches) is unchanged. This is the same class of slowdown as the 1.1.0 import-name fix, now closed for repeated method/symbol names. Tune the cutoff with `CODEGRAPH_AMBIGUOUS_NAME_CEILING` if you ever need to. Thanks @DANOX2 for the detailed report and repro. (#999)
 - Claude Code's front-load prompt hook now fires for non-English prompts. The optional hook that injects CodeGraph context for structural questions only recognized English keywords, so a structural question written in Chinese — or any non-Latin-script language — silently injected nothing: the hook looked like it wasn't wired up despite a correct setup, with no error to explain why. The gate is now language-aware. It recognizes Chinese structural keywords (如何/流程/调用/依赖/实现/架构…), and — in any language — a prompt that names a real code symbol from your project, such as `getUserId`, `article_publish`, `user.login`, or `parseToken()` (the name is checked against the index, so an ordinary word that merely looks like code doesn't trigger it). Non-structural prompts ("fix this typo", in any language) stay a no-op as before, so nothing fires where there's no structural answer to give. Thanks @whinc for the detailed report and repro. (#994)