fix(sync): filesystem-based change detection (catch git pull & non-git edits)

[colbymchenry]

Problem

Incremental sync (the file watcher and git hooks both call codegraph sync)
detected changes via git status --porcelain, which only reports uncommitted
working-tree changes. After a git pull / checkout / merge / rebase the
working tree is clean, so sync reconciled nothing and the index silently went
stale until a full codegraph index -f. Non-git projects also leaned on a slow
full-rescan path. Surfaced from #393.

Reproduced: commit a change (clean tree) → codegraph sync → the new symbol is
missed; only index -f picked it up.

Fix

• src/extraction/index.ts — change detection is now filesystem-based and
  git-independent. Enumerate current source files, skip unchanged ones with a
  cheap (size, mtime) stat pre-filter (both columns already stored per file),
  then confirm the rest with a content hash. Removals are checked against the
  filesystem (git ls-files still lists a file deleted-but-unstaged, so set
  membership alone misses deletions). This catches committed pull/checkout/merge/
  rebase changes, plain edits in non-git projects, adds, and deletes — uniformly.
• src/mcp/index.ts — catch-up sync on connect. CodeGraph.open() doesn't
  sync, so a non-blocking catchUpSync() now runs when a client connects,
  reconciling anything changed while the server was down (e.g. a terminal git pull). It logs Caught up N file(s) changed since last run and runs even when
  the watcher is unavailable (WSL2 /mnt), where it matters most.

The one theoretical blind spot is a content change that preserves both size and
mtime exactly — the same limitation every mtime-based incremental tool accepts;
codegraph index -f is the escape hatch (git bumps mtime on checkout, so pulls
are caught).

Validation

10-check suite (pull-like committed add, delete, non-git plain edit, no-op
incrementality with stable counts + intact edges, and catch-up-on-connect), plus
the full unit suite:

• ✅ macOS (FSEvents) — all cases + vitest 815 passed
• ✅ Linux (Docker node:22, inotify) — all 10 checks
• ✅ Windows 11 (ARM64 VM, ReadDirectoryChangesW) — all 10 checks

Notes / follow-ups

• getChangedFiles() (the codegraph status display helper) still uses git status, so status can under-report pending changes after a pull. Display-only;
  sync() itself is now correct. Left for a separate change.
• package.json is intentionally not bumped here — version bump + tag belong
  to the release commit/workflow.

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