Self-contained distribution: bundle Node + node:sqlite, drop better-sqlite3/wasm (closes #238) (#282)

* fix(db): eliminate concurrent-read "database is locked"; add node:sqlite backend (#238)

WAL + busy_timeout were already enabled, so the issue's suggested fix was a
no-op. The real causes, addressed here:

- busy_timeout is now set first (before journal_mode) and lowered 120s -> 5s,
  so open-time pragmas wait out a lock instead of hanging for two minutes.
- getCodeGraph no longer opens a second connection to the default project when
  a tool passes its own projectPath (the in-process lock amplifier).
- The wasm fallback (no WAL) gets a bounded read-retry on SQLITE_BUSY.
- New: node:sqlite backend, preferred over wasm, so installs whose native
  better-sqlite3 build fails land on a real-WAL backend instead of no-WAL wasm.
- codegraph status / codegraph_status now report the effective journal mode, so
  a lock report is triageable (wal vs delete).
- CLI hard-blocks Node < 20 to actually enforce the engines floor.

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

* refactor(db)!: node:sqlite is the sole backend; drop better-sqlite3 + wasm

Now that distribution will bundle a Node 24 runtime, node:sqlite (real SQLite
with WAL + FTS5) is always available. Collapse the three-backend adapter to
node:sqlite only and remove the machinery the other two needed:

- Remove better-sqlite3 (optionalDependency) and node-sqlite3-wasm (dependency).
- Remove WasmDatabaseAdapter, the named->positional param translation, the
  SQLITE_BUSY read-retry, the wasm fallback banner, the backend env override,
  and the native/node-sqlite/wasm selection chain.
- createDatabase now opens node:sqlite directly, with a clear error pointing at
  the bundled release / Node 22.5+ when the module is absent.
- NodeSqliteAdapter.close() is idempotent and pragma() supports { simple }, to
  match the better-sqlite3 behavior callers relied on.
- status (CLI + MCP) reports the single node:sqlite backend; journal-mode
  diagnostics and the getCodeGraph single-connection fix are retained.
- Tests repointed off better-sqlite3 onto node:sqlite.

Net -1044 lines. Running from source now requires Node 22.5+.

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

* feat(dist): self-contained bundle prototype (vendored Node + install channels)

Phase 3 of the node:sqlite migration: ship a vendored Node runtime so CodeGraph
runs with no system Node and no native build (node:sqlite is built in).

- scripts/build-bundle.sh: build a per-platform archive (official Node + dist +
  prod deps + launcher). Same recipe per platform; pins Node v24.16.0.
- install.sh: curl|sh installer (no Node required) — detects os/arch, pulls the
  archive from Releases, symlinks onto PATH; re-run to upgrade, --uninstall to
  remove. The VPS/SSH path.
- scripts/npm-shim.js: thin launcher for the npm channel — resolves the
  per-platform optionalDependency bundle and execs it, so `npm i -g` keeps
  working and the real work runs on the bundled Node regardless of the user's.
- BUNDLING.md: distribution design + release-pipeline TODO (CI matrix, platform
  packages, code signing, brew, retiring the Node-version gate).

Validated end-to-end: darwin-arm64 and linux-x64 bundles both run init + index +
status (Backend: node:sqlite, Journal: wal) + FTS query with NO system Node —
linux-x64 verified in a clean ubuntu:24.04 amd64 container. Release archives are
gitignored; CI will produce and upload them.

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

* feat(dist): add Windows PowerShell installer (install.ps1)

The `irm … | iex` one-liner for Windows, mirroring install.sh: detect arch,
pull the matching bundle from Releases, extract to %LOCALAPPDATA%\codegraph,
add it to user PATH. Re-run to upgrade. (Windows bundle production in
build-bundle.sh is still TODO.)

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

* feat(dist): release workflow + npm packaging; README/CHANGELOG for bundled distro

- .github/workflows/release.yml: manually-triggered (workflow_dispatch) release
  matrix. Builds a self-contained bundle per platform on its own runner
  (darwin-arm64/x64, linux-x64/arm64), publishes a GitHub Release with all
  archives, and publishes the npm thin-installer (shim + per-platform packages).
  Windows targets are TODO (build-bundle.sh is unix-only).
- scripts/pack-npm.sh: assemble the npm packages from built bundles — per-platform
  packages tagged os/cpu + the main shim package with them as optionalDependencies
  (esbuild pattern). Proven locally: npm-install the tarballs, run via the shim,
  resolves the bundle and runs on the bundled Node 24 (node:sqlite / WAL).
- README: install section now leads with the no-Node one-liners (curl|sh, irm|iex)
  then npm/npx; "bundled · none required" badge.
- CHANGELOG: standout headline for the self-contained release, plus Added/Changed/
  Removed for the install channels, node:sqlite backend, and dropped deps.

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

* feat(dist): Windows bundles + single-trigger release workflow

- build-bundle.sh: add win32-x64 / win32-arm64 targets — download Node's Windows
  zip, bundle node.exe + a .cmd launcher, output a .zip. Verified structurally
  (PE32+ node.exe, CRLF .cmd, portable node_modules). Since there are no native
  addons, any target builds on any OS, so the whole matrix builds on one runner.
- pack-npm.sh: handle .zip bundles and win32 packages (os: win32, node.exe).
- release.yml: simplified to your spec — manual trigger reads the version from
  package.json, builds all platform bundles, creates the GitHub Release with notes
  pulled from CHANGELOG.md, and publishes the npm shim + platform packages.
- BUNDLING.md: Windows + build-anywhere notes; release pipeline documented.

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

---------

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

src/mcp/tools.ts

@@ -11,7 +11,6 @@ import { writeFileSync, readFileSync, existsSync } from 'fs';
 import { clamp, validatePathWithinRoot } from '../utils';
 import { tmpdir } from 'os';
 import { join } from 'path';
-import { WASM_FALLBACK_FIX_RECIPE } from '../db';
 
 /** Maximum output length to prevent context bloat (characters) */
 const MAX_OUTPUT_LENGTH = 15000;
@@ -542,6 +541,17 @@ export class ToolHandler {
       throw new Error(`CodeGraph not initialized in ${projectPath}. Run 'codegraph init' in that project first.`);
     }
 
+    // If the path resolves to the default project, reuse the already-open
+    // default instance rather than opening a SECOND connection to the same DB.
+    // A duplicate connection serializes reads against the watcher's auto-sync
+    // writes; on the wasm backend (no WAL) that surfaces as intermittent
+    // "database is locked" on concurrent tool calls. See issue #238. Deliberately
+    // not cached under projectPath — the server owns and closes the default
+    // instance, so routing it through projectCache.closeAll() would double-close it.
+    if (this.cg && this.cg.getProjectRoot() === resolvedRoot) {
+      return this.cg;
+    }
+
     // Check if we already have this resolved root cached (different path, same project)
     if (this.projectCache.has(resolvedRoot)) {
       const cg = this.projectCache.get(resolvedRoot)!;
@@ -1321,16 +1331,21 @@ export class ToolHandler {
       `**Database size:** ${(stats.dbSizeBytes / 1024 / 1024).toFixed(2)} MB`,
     ];
 
-    // Surface the active SQLite backend. Without this, users on the
-    // silent WASM fallback (better-sqlite3 install failed) see "slow"
-    // indexing and DB-lock errors with no signal of why.
-    const backend = cg.getBackend();
-    if (backend === 'native') {
-      lines.push(`**Backend:** native (better-sqlite3)`);
+    // Surface the active SQLite backend (node:sqlite, Node's built-in real
+    // SQLite — full WAL + FTS5, no native build).
+    lines.push(`**Backend:** node:sqlite (Node built-in) — full WAL + FTS5`);
+
+    // Effective journal mode. 'wal' ⇒ concurrent reads never block on a writer;
+    // anything else ⇒ they can ("database is locked"). node:sqlite supports WAL
+    // everywhere, so a non-wal mode means the filesystem can't (network/
+    // virtualized mounts, WSL2 /mnt). See issue #238.
+    const journalMode = cg.getJournalMode();
+    if (journalMode === 'wal') {
+      lines.push(`**Journal mode:** wal (concurrent reads safe)`);
     } else {
       lines.push(
-        `**Backend:** ⚠ wasm (better-sqlite3 unavailable) — ` +
-        `5-10x slower than native. Fix: ${WASM_FALLBACK_FIX_RECIPE}`
+        `**Journal mode:** ⚠ ${journalMode || 'unknown'} — WAL not active, so reads ` +
+        `can block on a concurrent write (WAL appears unsupported on this filesystem)`
       );
     }