fix(reference): report entries beyond the path limit as I/O failures (#2716)

* fix(reference): report entries beyond the path limit as I/O failures

Reference-source traversal joins each child onto the root path. A valid
tree whose nested entries exceed the platform's absolute path limit
(PATH_MAX 1024 on macOS) makes lstat fail with ENAMETOOLONG. The
reader's filesystem error allow-list lacked that code, so
filesystemFailureDetail returned undefined and the native rejection
escaped both readReferenceSource and importReferenceSource instead of
becoming the existing failed `io` entry.

Add ENAMETOOLONG to the allow-list, matching the JavaScript application
reader's list. Readable siblings stay in the graph and the unreachable
entry is recorded with its OS message.

Fixes #2652

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

* test(reference): assert the imported graph keeps readable and failed entries

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

* fix(process): report no remaining time after a provider deadline fires

Node timers can fire while performance.now() is still a fraction of a
millisecond short of the monotonic deadline. ProviderStartupDeadline then
reported interruption "timeout" and an aborted signal while remainingMs()
returned ceil(0.x) = 1, so polling loops guarded by remainingMs() > 0
(Hopper and Ghidra startup) could run past an elapsed deadline, and the
real-timer test "aborts a bounded wait when its real monotonic deadline
expires" failed intermittently in CI (expected 1 to be 0).

Once the deadline's own timer has classified a timeout, report zero
remaining time. A deterministic regression test fires the timer with the
monotonic clock 0.4 ms short of the deadline.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

* fix(reference): preserve path limit entry uncertainty

* fix(reference): preserve unknown entry failures and identity

* fix(reference): type unknown-kind exclusions and keep them out of symlink counts

The metadata-failure path offers "unknown" to exclusion predicates, but
the predicate type only admitted concrete kinds, which broke the build.
Directory-only secret and ignore rules now also match an unknown-kind
entry (it may be a directory), and the summary counts unknown entries
separately instead of as symlinks.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
Co-authored-by: morluto <76467478+morluto@users.noreply.github.com>
Co-authored-by: Codex <codex@users.noreply.github.com>

src/reference/ReferenceSourceReaderTypes.ts

@@ -10,11 +10,17 @@ export type ReferenceSourceEntryKind =
   | "symlink"
   | "other";
 
+/**
+ * Kind offered to exclusion predicates. `unknown` marks an entry whose
+ * metadata could not be read, so its concrete kind cannot be claimed.
+ */
+export type ReferenceSourceExclusionKind = ReferenceSourceEntryKind | "unknown";
+
 export interface ReferenceSourceReaderOptions {
   readonly signal?: AbortSignal;
   readonly shouldExclude?: (
     path: string,
-    kind: ReferenceSourceEntryKind,
+    kind: ReferenceSourceExclusionKind,
   ) => boolean;
 }
 
@@ -84,7 +90,7 @@ export type TraversalState = {
   readonly signal?: AbortSignal;
   readonly shouldExclude?: (
     path: string,
-    kind: ReferenceSourceEntryKind,
+    kind: ReferenceSourceExclusionKind,
   ) => boolean;
   readonly entries: ReferenceSourceEntry[];
   readonly pending: PendingDirectory[];