fix(mcp): self-heal stale read-tool responses after external file edits

[zzet]

Problem

After an external file change — a native Edit/Write, a git checkout, or any edit that does not go through Gortex's own edit_file/write_file — the index-backed read tools (get_symbol_source, get_symbol, get_file_summary, get_editing_context, get_cfg) could return a stale body until the file watcher caught up. The visible symptom is a read returning an old symbol body while the file's metadata (e.g. line count) already reflects the new content.

Root cause

These tools call ensureFresh() to re-index a drifted file before serving it. But ensureFresh bailed out unconditionally whenever a multiIndexer was present:

if s.multiIndexer != nil {
    return nil
}

So in multi-repo mode the on-read self-heal did nothing at all. It had been disabled because the staleness check keyed off the lone single-Indexer, whose mtime map is empty for cross-repo paths — making IsStale true for every file, so the resulting mass re-index raced the live read surface and crashed the transport. It was switched off rather than fixed.

Fix

1. ensureFresh is now multi-repo-aware.
Each path is routed to its owning per-repo indexer (MultiIndexer.IndexerForFile), and re-indexed only when IsTrackedStale reports genuine drift. IsTrackedStale returns false for untracked / new / already-current files, so only a known-and-changed file is touched — no mass churn, which is what removes the original crash hazard. The recorded mtime is restamped after re-index so a follow-up read in the same window does no redundant work. Single-repo behaviour is unchanged (an active watcher still owns freshness, and the auto-refresh stands down rather than fight it).

2. read_file flags overlay-served responses.
When an editor-buffer overlay is active, read_file serves the buffer over disk; it now stamps served_from: "overlay" (plus an omission note) so an agent can tell a live buffer view from disk content. Drifted overlays were already rejected upstream by the overlay view guard, so this only annotates the live-buffer case.

Tests

• TestEnsureFresh_MultiRepoSelfHealsStaleFile — the regression test: a file changed on disk after indexing is re-indexed on read in multi-repo mode. Fails on the pre-fix code (which returned nil).
• TestEnsureFresh_SingleRepoSelfHealsStaleFile — same for the single-repo path.
• TestReadFile_FreshOverlayIsServed / TestReadFile_OverlayDriftSurfacesError — overlay provenance flag + the existing drift protection.
• The existing ensureFresh tests (watch-mode-skip, nil-indexer, rate-limit) still pass.

Verification

• go build -o /tmp/gortex-build ./cmd/gortex/ (CGO) — clean.
• go test -race ./internal/mcp/ — 2417 passed.
• golangci-lint / go vet — clean on the touched files.