fix(resolution): gate closure-collection synthesis to Swift/Kotlin and de-quadratic its line accounting (#1235) (#1237)

closureCollectionEdges scanned every method/function node in every
language, but its dispatcher patterns ({ $0( / { it( ) are Swift/Kotlin
trailing-closure syntax — on PHP/JS repos the pass can never emit an
edge, yet .push(/.add( fired its append gate on nearly every function.
Per match it computed the line via src.slice(0, idx).split('\n'), which
is O(source) per match and goes quadratic on match-dense generated
functions (two-byte content roughly doubles it). On a 12,860-file
PHP/JS app that was 20+ minutes of the "Resolving refs" tail — frozen
at 97% — and a #850 watchdog kill; profiled on CRMEB it was 127s of a
166s index for zero edges.

- Skip nodes whose language isn't swift/kotlin before any file I/O.
- makeLineAt(): lazy newline index + binary search, shared with the
  emitter passes' per-file lineOf.
- Yield every 256 regex matches inside the scan's match loops so a
  single pathological function can't starve the watchdog.

CRMEB (ThinkPHP, 2,913 files): 166.8s -> 72.7s, graph byte-identical.
Alamofire: closure-collection edges byte-identical (9 edges, 4 fields).
Drupal core control: graph byte-identical.

Co-authored-by: Claude Fable 5 <noreply@anthropic.com>

CHANGELOG.md

@@ -14,7 +14,7 @@ and adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ### Fixes
 
-- Indexing very large codebases no longer dies at the end of the "Resolving refs" step. Two failure modes are fixed: on multi-million-symbol projects (e.g. the Linux kernel, ~95,000 files) the final analysis phase ran out of memory and crashed the process outright, and on large projects on slower machines (reported on a 24,000-file Java project on Windows) the same phase could stall long enough that the safety watchdog killed a healthy, still-progressing index at ~98% (#1212). The whole phase now streams its work instead of holding whole-graph snapshots in memory, keeps the process responsive throughout, and skips analysis passes for languages a project doesn't contain — which also makes the tail of indexing noticeably faster on single-language repos. The resulting graph is identical, and a genuinely wedged process is still detected and killed.
+- Fixed `codegraph init` grinding for 20+ minutes (or getting killed by the safety watchdog) near the end of the "Resolving refs" step on large PHP and JavaScript codebases — a regression since 0.9.x reported on a 12,000-file project that used to index in about a minute. One of the dynamic-dispatch analysis passes only ever applies to Swift/Kotlin closure collections, but it was scanning every function in every language, and on `.push(`-heavy JavaScript (or any codebase with big generated functions, especially with non-ASCII text) its per-match bookkeeping went quadratic. The pass now skips languages it can't apply to, does its line accounting in constant time, and stays responsive even inside a single pathological function — the graph produced is identical. Thanks @sniperrenren for the report. (#1235) Two failure modes are fixed: on multi-million-symbol projects (e.g. the Linux kernel, ~95,000 files) the final analysis phase ran out of memory and crashed the process outright, and on large projects on slower machines (reported on a 24,000-file Java project on Windows) the same phase could stall long enough that the safety watchdog killed a healthy, still-progressing index at ~98% (#1212). The whole phase now streams its work instead of holding whole-graph snapshots in memory, keeps the process responsive throughout, and skips analysis passes for languages a project doesn't contain — which also makes the tail of indexing noticeably faster on single-language repos. The resulting graph is identical, and a genuinely wedged process is still detected and killed.
 - Indexing and `codegraph sync` stay responsive through their heaviest internal steps on huge projects: the post-index database maintenance (which on a multi-gigabyte index could stall the process for minutes and get a fully successful index killed by the safety watchdog at the finish line) now runs on a background thread, storing a giant generated file no longer freezes the process mid-extraction, and the reference-resolution bookkeeping between progress updates is broken into small responsive steps. The resulting graph is byte-for-byte identical.
 - Fixed a race that could leave a freshly-attached MCP session permanently silent: when a client's first messages arrived glued together during the daemon's connection handshake (roughly one attach in five on a busy machine), the daemon could drop them and stop reading that connection entirely — every tool call from that session then hung with no reply. The handshake now hands the connection over losslessly, and the fix is validated by hammering the previously-flaky attach test 25× under load.
 - The first tool call after the shared daemon starts no longer waits behind the query workers' cold start (which can take many seconds on a busy machine) — it's served directly until the first worker is warm, so a fresh session answers immediately.