fix(mcp): reap the server when its launcher is killed during startup (#1185) (#1199)

An MCP host that kills the launcher chain within the server's first ~100ms
while keeping the stdio pipes open (config probe, cancelled request, startup
timeout; Rust hosts that kill a child without dropping its stdio handles) left
the server orphaned: it booted already reparented to init, so the PPID
watchdog's "ppid changed" baseline was captured as 1 and could never fire, and
stdin never EOF'd. The process lingered — idle, ~30MB — until the host itself
exited, accumulating one per abandoned launch (the pile-up reported in #1185).
Reproduced on released 1.2.0/macOS: SIGKILL the launcher at +50ms → permanent
orphan; at +150ms the old late baseline had already run and reaped it.

Three-part fix:
- Capture process.ppid at the earliest line of the CLI entry (early-ppid.ts)
  and use it as every watchdog baseline, shrinking the blind window to the few
  ms before our first JS runs.
- Thread the real host pid down the bundled path: the npm shim and the
  standalone sh launcher set CODEGRAPH_HOST_PPID (an outer launcher's value
  wins), so the watchdog polls the host directly. Previously only the
  --liftoff-only relaunch set it, leaving the entire npm/standalone install
  base with hostPpid=null.
- Never-initialized backstop (startup-handshake.ts): a serve --mcp that
  receives no MCP traffic for CODEGRAPH_STARTUP_HANDSHAKE_TIMEOUT_MS (default
  15min, 0 disables) shuts down — the catch-all for a kill landing in the
  residual pre-JS window. Disarmed on the first byte, so a quiet-but-live
  session is never touched.

Also scrub CODEGRAPH_HOST_PPID from the detached daemon's env — it has no host,
and a stale pid must not leak into anything it spawns.

Validated end-to-end on the built bundle: the +50ms early-kill orphan is now
reaped while the host still holds the pipes open, and all six normal
lifecycle paths (clean close, SIGTERM/SIGKILL child, host exit/SIGKILL,
fd-holding adversarial host) stay clean. New coverage in
startup-handshake.test.ts, mcp-startup-orphan.test.ts, and npm-shim.test.ts.

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

CHANGELOG.md

@@ -36,6 +36,7 @@ and adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 - `codegraph init` and `codegraph index` no longer get killed by the safety watchdog at the "Resolving refs" step on large method-name-heavy codebases (big Java/enterprise monorepos were the main victims, especially on slower machines). Resolution used to come up for air only every 500 references, so a dense stretch of expensive ones could starve the watchdog long enough for it to assume the process was stuck and kill a perfectly healthy index. Resolution now checkpoints after every reference, and two of the expensive steps got much cheaper: repeated method lookups on the same type are now cached, and source files are no longer re-split line-by-line for every call being resolved — indexing such repos is several times faster as a result. Generated or minified single-line files are also skipped during receiver-type inference instead of being scanned per call. Thanks @UchihaYong and @wangmeng-95 for the reports. (#1122)
 - An index left incomplete by an interrupted run now heals itself on the next sync instead of silently staying wrong forever. If indexing died partway through resolving references (a crash, Ctrl-C, or the watchdog kill fixed above), the affected files still looked indexed but their caller/impact edges were missing — a too-small blast radius clustering by package or module, e.g. a Spring `@Resource`-injected method reporting 3 of its 10 real caller files — and because incremental syncs only re-resolve files that changed, the damage was permanent until a full re-index. Any sync (a watched file change, or a bare `codegraph sync`) now detects the leftover references and finishes resolving them, `codegraph status` warns when an index is in that state instead of passing it off as healthy, and a rare early-stop that could abandon resolution on repos whose first files reference only external libraries is fixed too. Thanks @KnifeOfLife for the report and the package-correlation observation that pinned it down. (#1187)
+- CodeGraph's background server no longer leaves a lingering Node process behind when your editor or agent kills its launcher during startup. If the app that started CodeGraph (Codex, Claude Code, or another MCP client) was killed within the server's first fraction of a second — a config probe, a cancelled request, a startup timeout — while keeping the connection's pipes open, the server could be handed off to the system before its orphan-detection watchdog had captured a reference point, leaving it running (idle, ~30 MB) until the launching app itself exited; over a long day of repeated launches these accumulated. The server now records its parent at the earliest possible moment, and the npm and standalone launchers pass the real host's process id down to it so it can watch the host directly instead of only the launcher that may already be gone. As a final backstop, a server that never receives a single request after starting now shuts itself down instead of waiting for the host to exit — tunable with `CODEGRAPH_STARTUP_HANDSHAKE_TIMEOUT_MS` (0 disables). Thanks @ruslan33321 for the report. (#1185)
 - The automatic context hook for Claude Code now fires for structural questions asked in nearly thirty languages — French, Spanish, Portuguese, German, Italian, Dutch, Polish, Czech, Romanian, Hungarian, Greek, Swedish, Danish, Norwegian, Finnish, Russian, Ukrainian, Turkish, Indonesian, Vietnamese, Thai, Hindi, Arabic, Farsi, Hebrew, Japanese, Korean, and both simplified and traditional Chinese — instead of just English and simplified Chinese. Previously a natural question like "comment marche la state machine des commandes ?" injected nothing unless it happened to contain a code-shaped symbol name, making the hook look broken for non-English teams. English questions phrased with derived word forms ("explain the architecture…", "what are the dependencies…") now fire too, and prompts in any other language still fire when they name a symbol from the index. Thanks @anthonyle-roy-lgtm for the report. (#1126)
 - Lua and Luau method calls with capitalized names (`obj:Method()` — the standard Roblox convention) now link to the right method. Because Lua's method-call syntax looks identical to a Luau type annotation, a capitalized call like `lg:Log()` was misread as declaring the variable's type, so whenever two or more classes shared a method name (`Init`, `Update`, `Destroy`, …) the call was silently dropped from callers, impact/blast-radius, and flow traces. Lowercase method names were unaffected. Thanks @inth3shadows for the precise root-cause analysis and repro. (#1124)
 - Removed dead code left behind by the discontinued managed-reasoning feature. Its `codegraph login` flow was unplugged before ever shipping in a release, but the unused module still shipped inside the platform bundles, and a security review flagged its Windows browser-open step (it routed the login URL through `cmd`, which would have been unsafe had the flow ever been wired back up). The leftover module and its tests are now fully deleted. Thanks @inth3shadows for the report. (#1114)