fix(mcp): normalize root-ish path filters in codegraph_files (#426) (#466)

The agent (opencode/Gemini Flash on Windows) called codegraph_files with
path="/" and got "No files found matching the criteria.", which pushed it
straight back to Read/Glob. Indexed file paths are stored as
project-relative POSIX (e.g. "src/foo.py"), and the old startsWith filter
matched nothing for any of the root-ish or platform-flavored shapes an
agent might guess: "/", ".", "./", "", "\\", leading-slash and
leading-./ subpaths, or Windows backslash subpaths.

Normalize the filter (strip leading "/", "./", "\", bare "."; convert
"\" to "/"; trim trailing "/"), then match by exact equal or "<filter>/"
boundary — which also kills a sibling-prefix bleed where filter "src"
used to match "src-utils/...".

Validated on macOS + Linux (Docker) + Windows (Parallels) with 13 new
unit tests plus the existing mcp-input-limits/concurrent-locking
suites, and end-to-end through opencode in tmux (Big Pickle/OpenCode
Zen): codegraph_files [path=/] now returns the project tree and the
agent answers directly instead of falling back to Read.

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

CHANGELOG.md

@@ -10,6 +10,7 @@ and adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 ## [Unreleased]
 
 ### Fixed
+- **`codegraph_files` now returns the whole project when an agent passes `path="/"`, `"."`, `"./"`, `""`, or a Windows-style `"\\"` — instead of "No files found matching the criteria."** Indexed file paths are stored as project-relative POSIX (e.g. `src/foo.ts`), but the path filter used a plain `startsWith`, so a leading slash or any of the other root-ish shapes an agent might guess matched nothing and pushed the agent back to Read/Glob — the exact opencode + Gemini Flash regression reported on Windows 11. Subdirectory filters are now equally forgiving: `"/src"`, `"./src"`, `"src/"`, `"src\\components"`, etc. all resolve correctly. Sibling-prefix bleed (`"src"` was previously matching `src-utils/...`) is also fixed — the filter now requires either an exact match or a `<filter>/` boundary. Closes #426.
 - **File watcher no longer marks edited files as fresh when another process holds the index lock.** When a second writer (concurrent `codegraph index`, a git hook, another MCP daemon) held `.codegraph/codegraph.lock`, `CodeGraph.sync()` returned a zero-shape no-op instead of throwing. The file watcher took that as a successful sync and cleared `pendingFiles` — so the per-file staleness signal MCP tools surface to agents (issue #403) dropped immediately, even though the edit was never indexed. `CodeGraph.watch()` now converts that no-op into a typed `LockUnavailableError` thrown into the watcher; the existing retry path preserves `pendingFiles` and reschedules until the lock becomes available. The error is logged at debug only (no `onSyncError` callback) so a long-running external indexer doesn't spam stderr every debounce cycle. Closes #449.
 - **Watch sync no longer aborts with `FOREIGN KEY constraint failed`.** PR #62 plugged this FK violation at the extraction layer (empty-named nodes whose containment edges had no target), but the same violation kept reappearing on v0.9.5 during the daemon's *watch sync* — not on initial index. Once an agent's daemon had been running long enough to accumulate edits, a resolver lookup that crossed a framework-specific cache could hand back a node whose row had been removed by a recent file rewrite, and the FK check then aborted the entire resolution batch, leaving the user's daemon log filling with `Watch sync failed { error: 'FOREIGN KEY constraint failed' }`. `QueryBuilder.insertEdges` now validates every batch's endpoints against the `nodes` table directly (one fresh `SELECT id IN (...)` per batch, no cache) and silently skips edges with missing source or target — so a stale lookup result drops one edge instead of aborting the whole sync. Surfaces as a fresh `codegraph init`/`index` cycle now surviving its first watch-sync cycle without the FK error, and the daemon recovering naturally instead of compounding into further failures. Closes #455.
 - **Hermes Agent: `codegraph install --target hermes` no longer corrupts `~/.hermes/config.yaml`.** Hermes serializes its config with PyYAML's default block style, which writes list items at the *same* indent as the parent mapping key (`cli:` and `- hermes-cli` both at column 2). The previous line-based YAML patcher mistook that first `  - hermes-cli` for the next sibling key, truncated the `cli:` block, and then spliced `- mcp-codegraph` at indent 4 *before* the existing items — leaving subsequent entries (`- browser`, `- clarify`, …) and even other platforms (`telegram:`, `discord:`) appearing at the `platform_toolsets:` level, which is no longer parseable YAML. The installer now recognizes the same-indent list style, finds the real end of the block at the next sibling key, and appends `- mcp-codegraph` at whatever indent the existing items already use. Re-installing on an already-corrupted file (or a 4-space-nested config that worked before) still produces a clean, parseable result. Closes #456.