fix(verify): distinguish appended exchanges from archive refreshes

[HengYangDS]

Problem

--verify treats archive mtime changes as an outdated index even when every exchange is indexed. Missing summaries can hide unindexed archives, and broad --repair can regenerate embeddings and summaries unnecessarily.

Change

• Compare parsed exchange lineEnd with the indexed high-water mark; distinguish appended content, unindexed archives, missing summaries and mtime-only refreshes.
• Verify an existing index read-only without creating an absent database. Lock-blocked verification exits 2 rather than reporting success.
• Preserve valid external-source rows, deduplicate repair candidates, and show actionable paths and the existing provider/embedding effects before repair.

archiveRefreshes is diagnostic, not a repair target. An unindexed status alone does not select a repair. Historical backfill remains outside this change. The direct repair test obtains its issue shape from the native verifier, avoiding a fixed field inventory.

Verification

Exact head: c8c190007661c50bafbb6753228658b6031b56e4; current target: 7e06519357777badd7a115d2014a7ef845904310.

Fresh qualification on 2026-10-10, macOS arm64, Node 22.23.3/npm 10.9.9:

• Independent empty-destination npm ci succeeds with this PR's unchanged manifest. Its native postinstall verifies the SQLite stack; dependencies are not borrowed from another PR.
• npm run build and original bundled-script syntax pass. The full npm test passes 356/356 across 63 files, zero skips, with every tracked input—including the original committed bundle—matching this exact head.
• The first cold-model suite retained two 10-second metadata-hook failures. Preparing the model through native initEmbeddings() and replaying the unchanged suite passes; no timeout or gate was loosened. Cold model preparation is therefore not claimed to fit those hooks.
• Resolved inputs include Transformers 4.3.1, better-sqlite3 12.11.1, TypeScript 5.9.3 and Vitest 3.2.7. The local resolver lock SHA-256 is f4ac20b63ee3980db1711ee636f8b79b56fdd6664e5c6cd50809d85722af9398; it is qualification evidence, not a repository lockfile change.

The declared Vitest 3 range has known dev-tool advisories (GHSA-82fw-gwwq-j7x9, GHSA-5gmw-xhrv-c9v3, GHSA-85c8-ppgw-ccpr). The operator accepted only trusted, isolated one-shot tests without credentials or a test server. Source dependencies and the live installation are unchanged; this is not security clearance for arbitrary input.

The earlier borrowed-tree Node matrix is not exact-input qualification. Current Node 24, hosted Linux/Windows, coverage and live-consumer acceptance are not verified. Exact-head CI remains action_required awaiting maintainer approval.

Integration

The unrelated committed MCP dependency drift is now removed: verifier and index-CLI modules are not reachable from MCP, so its bundle is byte-exact to the upstream base. No host-specific paths, policies or dependency upgrade are added. If #109 or #180 lands first, refresh shared verifier changes and rerun invalidated checks before merge. Maintainer merge and release remain separate outcomes.

Minimal-scope revision (2026-10-11)

Current exact head: ab29746447333ab3755a961713b75e454386556e; parent: c8c190007661c50bafbb6753228658b6031b56e4. The qualification above is historical evidence for that parent, not an exact-head claim for this follow-up.

• Restored only dist/mcp-server.js to the unchanged upstream 7e06519357777badd7a115d2014a7ef845904310 blob. All ten bundled product-source sections already matched upstream; original esbuild reachability excludes src/verify.ts and src/index-cli.ts. This removes unrelated dependency behavior/layout changes.
• All 211 other tracked files and executable modes remain exact parent bytes. The PR now contains nine focused source/dist/CLI/documentation/test files.
• Native npm run build, bundle syntax and 356/356 tests across 63 files, zero skips, including three actual packaged MCP tests, pass on existing workspace Node 24.19.0/npm 12.2.0, macOS arm64. The original MCP bundle is retained after the build; fresh resolver bytes are not claimed to reproduce an original official build.
• Reuses the same isolated native npm ci dependency tree qualified for fix(indexer): keep session indexing incremental on append #176; the three PRs have identical manifests and the prior resolver lock is unchanged. This is not a separate install, an official committed lock, a cold-model claim or hosted/Windows acceptance. The model cache is byte-qualified, native allowScripts and trusted-isolated-test risk limits stay unchanged, and owned test temporary state is removed with exact absence readback.

Current Node 24 local source/packaged acceptance is now proved; hosted CI/workflow approval, Windows, coverage, maintainer merge, stable release inclusion and installed-consumer adoption remain separate unverified gates. No duplicate approval ping accompanies this factual revision.

[HengYangDS]

Author follow-up for #177: the exact PR head is still mergeable, but its CI run remains action_required and has not executed. The consolidated current request on #180 covers this contribution as well: please approve the fork workflow and review its narrow source behavior for merge. I will address resulting failures and keep generated output, portability and generality qualified; no hosted pass or installation update is claimed.