From c43c5aa055835c81ed5f89da51ce26cd13a75fff Mon Sep 17 00:00:00 2001
From: Laith Al-Saadoon <alsaadoonlaith@gmail.com>
Date: Sun, 10 May 2026 04:11:40 +0000
Subject: [PATCH 01/10] fix(cli): scan ingests SARIF into the scanned repo, not
 CWD

`codehub scan <path>` only forwarded the `--repo NAME` flag to its
inner `runIngestSarif` call. When operators passed a positional
`<path>` instead, ingest-sarif fell back to `process.cwd()`, so
findings landed in the operator's CWD repo graph rather than the
repo that was actually scanned.

Fix: pass the already-resolved `repoPath` through. `runIngestSarif`
treats absolute paths as a registry-name fallback (ingest-sarif.ts:
351-352), so this works for both `--repo NAME` and positional `<path>`
invocations.

Found during the 2026-05-10 overnight smoke campaign on a TS auth
fixture under /tmp/. See journal.md (Bug #2) for the repro.
---
 packages/cli/src/commands/scan.ts | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/packages/cli/src/commands/scan.ts b/packages/cli/src/commands/scan.ts
index 05057867..7027331b 100644
--- a/packages/cli/src/commands/scan.ts
+++ b/packages/cli/src/commands/scan.ts
@@ -160,9 +160,13 @@ export async function runScan(path: string, opts: ScanOptions = {}): Promise<Sca
   await writeFile(outputPath, `${JSON.stringify(finalSarif, null, 2)}\n`, "utf8");
 
   // Ingest into the graph (best effort — missing graph is non-fatal).
+  // Forward the already-resolved `repoPath` so the SARIF lands in the
+  // SCANNED repo's graph, not the operator's CWD. `runIngestSarif`
+  // accepts an absolute path in `opts.repo` as a registry-name fallback
+  // (`ingest-sarif.ts:351-352`), so this works for both `--repo NAME`
+  // and positional `<path>` invocations.
   try {
-    const ingestOpts: { repo?: string; home?: string } = {};
-    if (opts.repo !== undefined) ingestOpts.repo = opts.repo;
+    const ingestOpts: { repo?: string; home?: string } = { repo: opts.repo ?? repoPath };
     if (opts.home !== undefined) ingestOpts.home = opts.home;
     await runIngestSarif(outputPath, ingestOpts);
   } catch (err) {

From c218c318db852bed0b53e51e998a06f27519721a Mon Sep 17 00:00:00 2001
From: Laith Al-Saadoon <alsaadoonlaith@gmail.com>
Date: Sun, 10 May 2026 04:11:56 +0000
Subject: [PATCH 02/10] fix(cli): doctor resolves native bindings from owner
 workspaces
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Under pnpm strict isolation, `tree-sitter*` is a direct dep of
`packages/ingestion`, `@duckdb/node-api` of `packages/storage`, and
`@ladybugdb/core` of `packages/storage` — none are direct deps of
`packages/cli` or the workspace root. The previous resolveFromRoot()
only tried the CLI's own require chain and the root package.json,
both of which fail under pnpm. Result: doctor printed
`tree-sitter or tree-sitter-typescript not installed` and similar
WARNs even when bindings were healthy and `pnpm -r test` was green.

Fix: extend resolveFromRoot with a per-workspace fallback that maps
native package families to their owner workspace's package.json,
so `createRequire(<owner>/package.json).resolve(pkg)` reliably
walks into the .pnpm store.

Also fix a latent crash in duckdbWorksCheck: @duckdb/node-api 1.x
exposes Sync teardown helpers (`disconnectSync`, `closeSync`); the
async `.close()` was dropped. Probe both, prefer Sync when present.
The previous fall-through-to-WARN had been masking this.

Found during the 2026-05-10 smoke campaign. See journal.md
(Bug #1, Bug #6) for the repros.
---
 packages/cli/src/commands/doctor.ts | 37 +++++++++++++++++++++++++----
 1 file changed, 33 insertions(+), 4 deletions(-)

diff --git a/packages/cli/src/commands/doctor.ts b/packages/cli/src/commands/doctor.ts
index 789e7ba2..6d886cf7 100644
--- a/packages/cli/src/commands/doctor.ts
+++ b/packages/cli/src/commands/doctor.ts
@@ -228,10 +228,17 @@ function duckdbWorksCheck(repoRoot: string): Check {
             hint: "run `pnpm install` at the repo root",
           };
         }
+        // The @duckdb/node-api 1.x surface exposes Sync teardown helpers
+        // (`disconnectSync`, `closeSync`). The async `.close()` accessors
+        // were dropped in 1.0.0; depending on them produced a false FAIL.
         const mod = (await import(duckPath)) as {
           DuckDBInstance: {
             create: (path: string) => Promise<{
-              connect: () => Promise<{ close: () => void | Promise<void> }>;
+              connect: () => Promise<{
+                disconnectSync?: () => void;
+                close?: () => void | Promise<void>;
+              }>;
+              closeSync?: () => void;
               close?: () => void | Promise<void>;
             }>;
           };
@@ -239,8 +246,10 @@ function duckdbWorksCheck(repoRoot: string): Check {
         // In-memory instance: never touches disk, never lingers.
         const inst = await mod.DuckDBInstance.create(":memory:");
         const conn = await inst.connect();
-        await conn.close();
-        if (typeof inst.close === "function") await inst.close();
+        if (typeof conn.disconnectSync === "function") conn.disconnectSync();
+        else if (typeof conn.close === "function") await conn.close();
+        if (typeof inst.closeSync === "function") inst.closeSync();
+        else if (typeof inst.close === "function") await inst.close();
         return { status: "ok", message: "duckdb open/close OK" };
       } catch (err) {
         return {
@@ -504,6 +513,26 @@ function resolveFromRoot(repoRoot: string, pkg: string): string | null {
     const req = createRequire(join(repoRoot, "package.json"));
     return req.resolve(pkg);
   } catch {
-    return null;
+    // fall through to per-package fallbacks
   }
+  // 3. Per-workspace fallback. Under pnpm strict isolation, native bindings
+  //    are direct deps of the package that uses them — `tree-sitter*` lives
+  //    in `packages/ingestion`, `@duckdb/node-api` in `packages/storage`.
+  //    Probing those package.json contexts lets `codehub doctor` resolve
+  //    the bindings even when neither the CLI nor the workspace root
+  //    declare them as direct deps.
+  const owners = pkg.startsWith("@duckdb/") || pkg.startsWith("@ladybugdb/")
+    ? ["packages/storage"]
+    : pkg.startsWith("tree-sitter")
+      ? ["packages/ingestion"]
+      : [];
+  for (const owner of owners) {
+    try {
+      const req = createRequire(join(repoRoot, owner, "package.json"));
+      return req.resolve(pkg);
+    } catch {
+      // try next
+    }
+  }
+  return null;
 }

From 433f68436c95862b93c2a9b3a82c0bfa0ee11aad Mon Sep 17 00:00:00 2001
From: Laith Al-Saadoon <alsaadoonlaith@gmail.com>
Date: Sun, 10 May 2026 04:12:24 +0000
Subject: [PATCH 03/10] fix(repo): smoke-mcp asserts 29 tools, matching the
 v1.0 server

The MCP server registers 29 tools at packages/mcp/src/server.ts:
list_repos, pack_codebase, query, context, impact, detect_changes,
rename, sql, group_list, group_query, group_status, group_contracts,
group_cross_repo_links, group_sync, project_profile, dependencies,
license_audit, owners, list_findings, list_findings_delta,
list_dead_code, remove_dead_code, scan, verdict, risk_trends,
route_map, api_impact, shape_check, tool_map.

scripts/smoke-mcp.sh still hard-coded EXPECTED_TOOLS=19, so
\`codehub bench\` reported the MCP-stdio gate as FAIL even when
the server was healthy. EXPECTED_TOOLS env-var override remains
for mid-migration windows.

Found during the 2026-05-10 smoke campaign. See journal.md (Bug #3).
---
 packages/cli/src/commands/doctor.ts | 11 ++++++-----
 scripts/smoke-mcp.sh                | 14 +++++++++-----
 2 files changed, 15 insertions(+), 10 deletions(-)

diff --git a/packages/cli/src/commands/doctor.ts b/packages/cli/src/commands/doctor.ts
index 6d886cf7..670e849a 100644
--- a/packages/cli/src/commands/doctor.ts
+++ b/packages/cli/src/commands/doctor.ts
@@ -521,11 +521,12 @@ function resolveFromRoot(repoRoot: string, pkg: string): string | null {
   //    Probing those package.json contexts lets `codehub doctor` resolve
   //    the bindings even when neither the CLI nor the workspace root
   //    declare them as direct deps.
-  const owners = pkg.startsWith("@duckdb/") || pkg.startsWith("@ladybugdb/")
-    ? ["packages/storage"]
-    : pkg.startsWith("tree-sitter")
-      ? ["packages/ingestion"]
-      : [];
+  const owners =
+    pkg.startsWith("@duckdb/") || pkg.startsWith("@ladybugdb/")
+      ? ["packages/storage"]
+      : pkg.startsWith("tree-sitter")
+        ? ["packages/ingestion"]
+        : [];
   for (const owner of owners) {
     try {
       const req = createRequire(join(repoRoot, owner, "package.json"));
diff --git a/scripts/smoke-mcp.sh b/scripts/smoke-mcp.sh
index ec63a8ff..1c3b5496 100755
--- a/scripts/smoke-mcp.sh
+++ b/scripts/smoke-mcp.sh
@@ -5,14 +5,18 @@
 # Uses only node (for the server) and python3 (for JSON parsing) — no extra
 # dependencies. Safe to run in CI.
 #
-# Tool roster at v1.0 (19 tools):
-#   Core (7): list_repos, query, context, impact, detect_changes, rename, sql
-#   Groups (4): group_list, group_query, group_status, group_contracts
+# Tool roster at v1.0 (29 tools — see packages/mcp/src/server.ts):
+#   Core (8): list_repos, pack_codebase, query, context, impact,
+#             detect_changes, rename, sql
+#   Groups (6): group_list, group_query, group_status, group_contracts,
+#               group_cross_repo_links, group_sync
 #   Project (1): project_profile
 #   Dependencies (2): dependencies, license_audit
 #   Ownership (1): owners
-#   Findings (2): list_findings, scan
+#   Findings (5): list_findings, list_findings_delta, list_dead_code,
+#                 remove_dead_code, scan
 #   Analysis (2): verdict, risk_trends
+#   Routing/contracts (4): route_map, api_impact, shape_check, tool_map
 #
 # CI / acceptance.sh can override the assertion via the EXPECTED_TOOLS env var
 # when the wire is mid-migration.
@@ -57,7 +61,7 @@ for line in sys.stdin:
 print(tools)
 ')
 
-EXPECTED_TOOLS="${EXPECTED_TOOLS:-19}"
+EXPECTED_TOOLS="${EXPECTED_TOOLS:-29}"
 if [ "$COUNT" = "$EXPECTED_TOOLS" ]; then
   echo "smoke-mcp: PASS ($COUNT tools listed)"
   exit 0

From fad766f0047d2919f391c8d95be20d3272523635 Mon Sep 17 00:00:00 2001
From: Laith Al-Saadoon <alsaadoonlaith@gmail.com>
Date: Sun, 10 May 2026 16:30:58 +0000
Subject: [PATCH 04/10] chore(repo): scrub spec coordinates from
 m7-parity-audit header
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Per the durable lesson "no spec-coordinate leakage into source" —
spec-coordinate prefixes belong in PR bodies and commit messages, not in
script comment headers where LLM clients pick them up and start citing
them back. Cleaned two stale references in scripts/m7-parity-audit.sh.
---
 scripts/m7-parity-audit.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/scripts/m7-parity-audit.sh b/scripts/m7-parity-audit.sh
index 6e64206a..09288f4e 100755
--- a/scripts/m7-parity-audit.sh
+++ b/scripts/m7-parity-audit.sh
@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-# scripts/m7-parity-audit.sh — graphHash byte-identity audit across backends (AC-A-10).
+# scripts/m7-parity-audit.sh — graphHash byte-identity audit across backends.
 #
 # Runs `codehub analyze --force` on the same corpus under BOTH:
 #   - `CODEHUB_STORE=duck`  → DuckDB legacy graph store
@@ -7,8 +7,8 @@
 #
 # Then extracts the `graph <hash>` line from each invocation's stderr and
 # asserts byte-identity. This is the whole-pipeline end-to-end companion to
-# the in-memory `assertGraphParity` harness (AC-A-7) — together they pin the
-# U1 (graphHash byte-identity) invariant from BOTH layers: in-memory
+# the in-memory `assertGraphParity` harness — together they pin the
+# graphHash byte-identity invariant from BOTH layers: in-memory
 # fixtures AND a real `codehub analyze` against a real corpus on disk.
 #
 # Usage:

From c5f9047ed7e53614f38aee54e56311c79568a4e2 Mon Sep 17 00:00:00 2001
From: Laith Al-Saadoon <alsaadoonlaith@gmail.com>
Date: Sun, 10 May 2026 16:32:12 +0000
Subject: [PATCH 05/10] fix(cli): bench dashboard surfaces all 17 acceptance
 gates

Before: MVP_GATES held 9 entries with stale titles
("graphHash determinism", "incremental reindex timings (soft)",
"Python eval harness") that diverged from the script banners,
so even those rows never advanced past pending. Net: 0 of 17
gates rendered correctly in `codehub bench`.

After: MVP_GATES mirrors all 17 banners from
scripts/acceptance.sh verbatim (gates 1-17 in script order),
with stable kebab-case ids. applyLine now also recognizes the
[SKIP] marker so graceful-degrade gates (eval, embeddings,
scanner-smoke, etc.) render as skipped rather than pending.
Updated unit tests to assert the new 17-gate roster, banner
format (N/17:), and SKIP-handling path.
---
 packages/cli/src/commands/bench.test.ts | 91 ++++++++++++++++---------
 packages/cli/src/commands/bench.ts      | 26 +++++--
 2 files changed, 79 insertions(+), 38 deletions(-)

diff --git a/packages/cli/src/commands/bench.test.ts b/packages/cli/src/commands/bench.test.ts
index ef794795..c8216786 100644
--- a/packages/cli/src/commands/bench.test.ts
+++ b/packages/cli/src/commands/bench.test.ts
@@ -7,7 +7,7 @@
  *     table;
  *   - the script-location fallback when the user passes an explicit
  *     --acceptance path;
- *   - the gate roster itself (9 gates, stable order).
+ *   - the gate roster itself (17 gates, stable order).
  */
 
 import { strict as assert } from "node:assert";
@@ -27,15 +27,15 @@ function freshRows(): GateRow[] {
   }));
 }
 
-test("MVP_GATES roster has 9 gates in stable order", () => {
-  assert.equal(MVP_GATES.length, 9);
+test("MVP_GATES roster has 17 gates in stable order", () => {
+  assert.equal(MVP_GATES.length, 17);
   assert.equal(MVP_GATES[0]?.id, "install");
-  assert.equal(MVP_GATES[MVP_GATES.length - 1]?.id, "eval");
+  assert.equal(MVP_GATES[MVP_GATES.length - 1]?.id, "m7-parity-audit");
 });
 
 test("applyLine flags a gate PASS when banner + marker sequence is seen", () => {
   const rows = freshRows();
-  applyLine(rows, "1/9: pnpm install --frozen-lockfile");
+  applyLine(rows, "1/17: pnpm install --frozen-lockfile");
   applyLine(rows, "  [PASS] install green");
   const install = rows.find((r) => r.id === "install");
   assert.ok(install);
@@ -45,7 +45,7 @@ test("applyLine flags a gate PASS when banner + marker sequence is seen", () =>
 
 test("applyLine flags a gate FAIL when marker follows banner", () => {
   const rows = freshRows();
-  applyLine(rows, "2/9: pnpm -r build");
+  applyLine(rows, "2/17: pnpm -r build");
   applyLine(rows, "  [FAIL] build failed");
   const build = rows.find((r) => r.id === "build");
   assert.ok(build);
@@ -53,6 +53,16 @@ test("applyLine flags a gate FAIL when marker follows banner", () => {
   assert.equal(build.detail, "build failed");
 });
 
+test("applyLine flags a gate SKIP when marker follows banner", () => {
+  const rows = freshRows();
+  applyLine(rows, "12/17: scanner smoke (semgrep)");
+  applyLine(rows, "  [SKIP] semgrep not installed");
+  const scanner = rows.find((r) => r.id === "scanner-smoke");
+  assert.ok(scanner);
+  assert.equal(scanner.status, "skipped");
+  assert.equal(scanner.detail, "semgrep not installed");
+});
+
 test("applyLine ignores markers without a preceding banner", () => {
   const rows = freshRows();
   applyLine(rows, "  [PASS] orphaned marker");
@@ -65,40 +75,53 @@ test("applyLine ignores markers without a preceding banner", () => {
 
 test("applyLine advances through every gate in a typical run", () => {
   const rows = freshRows();
+  // Real banner+marker pairs straight from scripts/acceptance.sh. Titles
+  // now match MVP_GATES verbatim, so every line should flip its row.
   const lines = [
-    "1/9: pnpm install --frozen-lockfile",
+    "1/17: pnpm install --frozen-lockfile",
     "  [PASS] install green",
-    "2/9: pnpm -r build",
+    "2/17: pnpm -r build",
     "  [PASS] build green",
-    "3/9: pnpm -r test",
+    "3/17: pnpm -r test",
     "  [PASS] all package tests pass",
-    "4/9: banned-strings grep",
+    "4/17: banned-strings grep",
     "  [PASS] banned-strings clean",
-    "5/9: license allowlist",
+    "5/17: license allowlist",
     "  [PASS] licenses within allowlist",
-    "6/9: determinism (double-run graphHash)",
+    "6/17: determinism (double-run graphHash)",
     "  [PASS] graphHash identical (abcd1234)",
-    "7/9: incremental reindex timings",
-    "  [PASS] timings captured (p95 ≤ 5s is a soft target at MVP; see docs)",
-    "8/9: MCP stdio boot smoke",
-    "  [PASS] MCP server boots and lists 7 tools",
-    "9/9: Python eval harness (49 parametrized cases)",
-    "  [PASS] eval: 49/49 cases passed",
+    "7/17: incremental reindex timings",
+    "  [PASS] timings captured",
+    "8/17: MCP stdio boot smoke",
+    "  [PASS] MCP server boots",
+    "9/17: Python eval harness (moved to opencodehub-testbed)",
+    "  [SKIP] harness lives in sibling repo",
+    "10/17: embeddings determinism",
+    "  [SKIP] no embedder weights",
+    "11/17: incremental timing on 100-file fixture",
+    "  [PASS] p95 within budget",
+    "12/17: scanner smoke (semgrep)",
+    "  [SKIP] semgrep not installed",
+    "13/17: SARIF schema validation",
+    "  [PASS] sarif schema valid",
+    "14/17: license-audit smoke",
+    "  [PASS] audit emitted",
+    "15/17: verdict smoke (2-commit fixture)",
+    "  [PASS] verdict tier=safe",
+    "16/17: pack-determinism (code-pack ×2 → diff -r)",
+    "  [PASS] pack identical",
+    "17/17: m7-parity-audit (analyze ×2 backends → graphHash)",
+    "  [PASS] graph parity holds",
   ];
-  // acceptance.sh titles have different trailing suffixes than MVP_GATES;
-  // applyLine matches by exact title, so lines that don't match simply
-  // leave the row pending. Verify that our title catalog is in sync by
-  // running through the intended titles directly.
-  for (const row of rows) {
-    applyLine(rows, `1/9: ${row.title}`);
-    applyLine(rows, `  [PASS] ${row.id} fake-detail`);
-  }
+  for (const l of lines) applyLine(rows, l);
+  // Every row should be either pass or skipped — no row left pending.
   for (const row of rows) {
-    assert.equal(row.status, "pass", `${row.id} should be pass`);
-    assert.match(row.detail, /fake-detail/);
+    assert.notEqual(row.status, "pending", `${row.id} should not be pending`);
+    assert.notEqual(row.status, "fail", `${row.id} should not be fail`);
   }
-  // Sanity: the real lines above do not throw.
-  for (const l of lines) applyLine(rows, l);
+  // At least one of each terminal status was exercised.
+  assert.ok(rows.some((r) => r.status === "pass"));
+  assert.ok(rows.some((r) => r.status === "skipped"));
 });
 
 test("locateAcceptanceScript honors an explicit --acceptance path", async () => {
@@ -134,9 +157,9 @@ test("runBench captures PASS output from a stubbed acceptance script", async ()
   const dir = await mkdtemp(join(tmpdir(), "codehub-bench-stub-"));
   try {
     const script = join(dir, "fake.sh");
-    // Emit a banner + PASS for each of the 9 gates so every row flips.
+    // Emit a banner + PASS for each of the 17 gates so every row flips.
     const body = MVP_GATES.map(
-      (g, i) => `echo "${i + 1}/9: ${g.title}"\necho "  [PASS] fake-${g.id}"`,
+      (g, i) => `echo "${i + 1}/17: ${g.title}"\necho "  [PASS] fake-${g.id}"`,
     ).join("\n");
     await writeFile(script, `#!/usr/bin/env bash\n${body}\nexit 0\n`);
     await chmod(script, 0o755);
@@ -157,9 +180,9 @@ test("runBench reports exitCode=1 when any gate fails", async () => {
   try {
     const script = join(dir, "fake.sh");
     const lines: string[] = [];
-    lines.push(`echo "1/9: ${MVP_GATES[0]?.title}"`, `echo "  [FAIL] boom"`);
+    lines.push(`echo "1/17: ${MVP_GATES[0]?.title}"`, `echo "  [FAIL] boom"`);
     for (let i = 1; i < MVP_GATES.length; i += 1) {
-      lines.push(`echo "${i + 1}/9: ${MVP_GATES[i]?.title}"`, `echo "  [PASS] ok"`);
+      lines.push(`echo "${i + 1}/17: ${MVP_GATES[i]?.title}"`, `echo "  [PASS] ok"`);
     }
     await writeFile(script, `#!/usr/bin/env bash\n${lines.join("\n")}\nexit 1\n`);
     await chmod(script, 0o755);
diff --git a/packages/cli/src/commands/bench.ts b/packages/cli/src/commands/bench.ts
index a0d502a1..3150db9d 100644
--- a/packages/cli/src/commands/bench.ts
+++ b/packages/cli/src/commands/bench.ts
@@ -56,10 +56,18 @@ export const MVP_GATES: readonly { readonly id: string; readonly title: string }
   { id: "tests", title: "pnpm -r test" },
   { id: "banned-strings", title: "banned-strings grep" },
   { id: "licenses", title: "license allowlist" },
-  { id: "determinism", title: "graphHash determinism" },
-  { id: "incremental", title: "incremental reindex timings (soft)" },
+  { id: "determinism", title: "determinism (double-run graphHash)" },
+  { id: "incremental", title: "incremental reindex timings" },
   { id: "mcp-smoke", title: "MCP stdio boot smoke" },
-  { id: "eval", title: "Python eval harness" },
+  { id: "eval", title: "Python eval harness (moved to opencodehub-testbed)" },
+  { id: "embeddings-determinism", title: "embeddings determinism" },
+  { id: "incremental-timing", title: "incremental timing on 100-file fixture" },
+  { id: "scanner-smoke", title: "scanner smoke (semgrep)" },
+  { id: "sarif-validation", title: "SARIF schema validation" },
+  { id: "license-audit-smoke", title: "license-audit smoke" },
+  { id: "verdict-smoke", title: "verdict smoke (2-commit fixture)" },
+  { id: "pack-determinism", title: "pack-determinism (code-pack ×2 → diff -r)" },
+  { id: "m7-parity-audit", title: "m7-parity-audit (analyze ×2 backends → graphHash)" },
 ];
 
 /**
@@ -205,7 +213,7 @@ function runScript(scriptPath: string): ScriptStream {
 
 /**
  * Apply a single line from `acceptance.sh` to the gate table. We parse
- * the `N/9: <title>` banner line to pick which row the next `[PASS] ...`
+ * the `N/17: <title>` banner line to pick which row the next `[PASS] ...`
  * or `[FAIL] ...` marker belongs to. Anything else is ignored (timing
  * summaries live under a gate row as `......` notes).
  */
@@ -239,6 +247,16 @@ export function applyLine(rows: GateRow[], rawLine: string): void {
     currentGateIdx = -1;
     return;
   }
+  const skipMatch = /^\s*\[SKIP\]\s+(.*)$/.exec(line);
+  if (skipMatch && currentGateIdx >= 0) {
+    const row = rows[currentGateIdx];
+    if (row) {
+      row.status = "skipped";
+      row.detail = skipMatch[1] ?? "";
+    }
+    currentGateIdx = -1;
+    return;
+  }
 }
 
 async function waitUntil(predicate: () => boolean): Promise<void> {

From 317bdf182d0225910f1dc7bf4ffcf13e8838c5ab Mon Sep 17 00:00:00 2001
From: Laith Al-Saadoon <alsaadoonlaith@gmail.com>
Date: Sun, 10 May 2026 16:33:24 +0000
Subject: [PATCH 06/10] fix(embedder): isolate http-embedder tests from
 operator env
MIME-Version: 1.0
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Content-Transfer-Encoding: 8bit

The `tryOpenHttpEmbedder` describe block had two cases that asserted a
`null` return when the HTTP env vars (`CODEHUB_EMBEDDING_URL`,
`CODEHUB_EMBEDDING_MODEL`) were absent. The pre-fix `beforeEach` only
deleted those two keys, leaving the SageMaker family
(`CODEHUB_EMBEDDING_SAGEMAKER_ENDPOINT`) untouched. Because
`tryOpenHttpEmbedder` consults SageMaker env first, an operator shell
exporting `CODEHUB_EMBEDDING_SAGEMAKER_ENDPOINT` flipped the assertion
target from `null` to `Promise<Embedder>` and the cases failed.

Fix: introduce `sanitizeEmbeddingEnv()` — a snapshot-and-wipe helper
that walks `process.env` and removes every `CODEHUB_EMBEDDING_*` key at
test entry, returning a restorer the `afterEach` calls. Wire it into
the `readHttpEmbedderConfigFromEnv`, `openEmbedder factory`, and
`tryOpenHttpEmbedder` describe blocks so all three are hermetic against
operator-shell leakage.

Verified with:
  CODEHUB_EMBEDDING_SAGEMAKER_ENDPOINT=fake-endpoint \
    pnpm -F @opencodehub/embedder test  # 79 pass, 0 fail
  pnpm -F @opencodehub/embedder test     # 79 pass, 0 fail
---
 packages/embedder/src/http-embedder.test.ts | 75 +++++++++++++--------
 1 file changed, 47 insertions(+), 28 deletions(-)

diff --git a/packages/embedder/src/http-embedder.test.ts b/packages/embedder/src/http-embedder.test.ts
index 0f3e5218..31f502aa 100644
--- a/packages/embedder/src/http-embedder.test.ts
+++ b/packages/embedder/src/http-embedder.test.ts
@@ -23,6 +23,38 @@ import {
   tryOpenHttpEmbedder,
 } from "./index.js";
 
+/**
+ * Snapshot-and-wipe every `CODEHUB_EMBEDDING_*` env var so tests are
+ * hermetic against an operator shell that exports `*_SAGEMAKER_ENDPOINT`,
+ * `*_URL`, `*_MODEL`, etc. Returns a restorer the caller invokes from
+ * `afterEach` (or a `finally`). Mirrors the existing originalHome pattern
+ * but covers the full `CODEHUB_EMBEDDING_*` namespace, since selection
+ * precedence in `tryOpenHttpEmbedder` checks SageMaker env BEFORE the HTTP
+ * env vars — a leaked `*_SAGEMAKER_ENDPOINT` flips a `null` assertion to
+ * a `Promise<Embedder>` and the case fails.
+ */
+function sanitizeEmbeddingEnv(): () => void {
+  const saved: Record<string, string | undefined> = {};
+  for (const k of Object.keys(process.env)) {
+    if (k.startsWith("CODEHUB_EMBEDDING_")) {
+      saved[k] = process.env[k];
+      delete process.env[k];
+    }
+  }
+  return () => {
+    // Wipe any keys the test set so they do not leak across cases.
+    for (const k of Object.keys(process.env)) {
+      if (k.startsWith("CODEHUB_EMBEDDING_") && !(k in saved)) {
+        delete process.env[k];
+      }
+    }
+    for (const [k, v] of Object.entries(saved)) {
+      if (v === undefined) delete process.env[k];
+      else process.env[k] = v;
+    }
+  };
+}
+
 /** Build a fetch mock that returns a JSON body with the given embedding. */
 function makeFetchMockOk(embedding: readonly number[]): typeof fetch {
   return async (_url, _init): Promise<Response> => {
@@ -352,26 +384,13 @@ describe("openHttpEmbedder: malformed body", () => {
 // ────────────────────────────────────────────────────────────────────
 
 describe("readHttpEmbedderConfigFromEnv", () => {
-  let originals: Record<string, string | undefined>;
+  let restoreEnv: () => void;
 
   beforeEach(() => {
-    originals = {
-      url: process.env["CODEHUB_EMBEDDING_URL"],
-      model: process.env["CODEHUB_EMBEDDING_MODEL"],
-      dims: process.env["CODEHUB_EMBEDDING_DIMS"],
-      key: process.env["CODEHUB_EMBEDDING_API_KEY"],
-    };
-    delete process.env["CODEHUB_EMBEDDING_URL"];
-    delete process.env["CODEHUB_EMBEDDING_MODEL"];
-    delete process.env["CODEHUB_EMBEDDING_DIMS"];
-    delete process.env["CODEHUB_EMBEDDING_API_KEY"];
+    restoreEnv = sanitizeEmbeddingEnv();
   });
   afterEach(() => {
-    for (const [k, v] of Object.entries(originals)) {
-      const envKey = `CODEHUB_EMBEDDING_${k === "key" ? "API_KEY" : k.toUpperCase()}`;
-      if (v === undefined) delete process.env[envKey];
-      else process.env[envKey] = v;
-    }
+    restoreEnv();
   });
 
   it("returns null when URL or MODEL is unset", () => {
@@ -429,6 +448,15 @@ describe("readHttpEmbedderConfigFromEnv", () => {
 // ────────────────────────────────────────────────────────────────────
 
 describe("openEmbedder factory", () => {
+  let restoreEnv: () => void;
+
+  beforeEach(() => {
+    restoreEnv = sanitizeEmbeddingEnv();
+  });
+  afterEach(() => {
+    restoreEnv();
+  });
+
   it("picks HTTP when endpointUrl is set", async () => {
     const embedder = await openEmbedder({
       endpointUrl: "https://embed.example/v1",
@@ -482,22 +510,13 @@ describe("openEmbedder factory", () => {
 });
 
 describe("tryOpenHttpEmbedder", () => {
-  let originals: Record<string, string | undefined>;
+  let restoreEnv: () => void;
 
   beforeEach(() => {
-    originals = {
-      url: process.env["CODEHUB_EMBEDDING_URL"],
-      model: process.env["CODEHUB_EMBEDDING_MODEL"],
-    };
-    delete process.env["CODEHUB_EMBEDDING_URL"];
-    delete process.env["CODEHUB_EMBEDDING_MODEL"];
+    restoreEnv = sanitizeEmbeddingEnv();
   });
   afterEach(() => {
-    for (const [k, v] of Object.entries(originals)) {
-      const envKey = `CODEHUB_EMBEDDING_${k.toUpperCase()}`;
-      if (v === undefined) delete process.env[envKey];
-      else process.env[envKey] = v;
-    }
+    restoreEnv();
   });
 
   it("returns null when env is not configured", () => {

From 898192eafe418b2d410b9847e21648f64fd2e5e4 Mon Sep 17 00:00:00 2001
From: Laith Al-Saadoon <alsaadoonlaith@gmail.com>
Date: Sun, 10 May 2026 16:36:07 +0000
Subject: [PATCH 07/10] docs(repo): README v1.0 status, 29 tools, parse-runtime
 + accurate package list

- Status flips from "v0.1.0 initial release" to "v1 feature-complete on
  M1-M7" with the 0.1.1 tag still shipped pending 1.0.0 sign-off.
- MCP tool surface bumped 28 -> 29 tools (matches
  packages/mcp/src/server.ts), with the federation, pack, and remaining
  tools enumerated explicitly.
- Repository layout regenerated against `ls packages/` -- now lists 17
  packages (cobol-proleap, frameworks, pack, policy, wiki added; eval
  and gym dropped to a sibling testbed).
- 14 -> 15 GA languages (COBOL via the regex provider).
- New "Parse runtime" section mirrors CLAUDE.md: WASM default, native
  opt-in via OCH_NATIVE_PARSER=1, complexity phase still native.
- Quick start: Node 22 or 24 (was Node 20+), Python 3.12 only for the
  SCIP indexers.
---
 README.md | 82 +++++++++++++++++++++++++++++++++++++++----------------
 1 file changed, 58 insertions(+), 24 deletions(-)

diff --git a/README.md b/README.md
index 9168f1e1..f791c7fc 100644
--- a/README.md
+++ b/README.md
@@ -60,7 +60,7 @@ flowchart LR
   C -->|detect communities + flows| E[Processes / clusters]
   D --> F[MCP server]
   E --> F
-  F -->|28 tools| G[AI coding agent]
+  F -->|29 tools| G[AI coding agent]
 ```
 
 ## Design choices worth knowing
@@ -71,13 +71,16 @@ flowchart LR
 | **Local-first, offline-capable** | `codehub analyze --offline` opens zero sockets. Your code never leaves your machine. No telemetry. |
 | **Deterministic indexing** | Identical inputs produce a byte-identical graph hash. Reproducible. Auditable. Cacheable in CI. |
 | **MCP-native** | Works out-of-the-box with Claude Code, Cursor, Codex, Windsurf, OpenCode. The MCP server is the primary interface; CLI exists for scripts and CI. |
-| **Embedded storage** | DuckDB + `hnsw_acorn` (filter-aware HNSW via ACORN-1 + RaBitQ) + `fts` (BM25). One file. No daemon. No database to operate. |
-| **14 languages at GA** | TypeScript, JavaScript, Python, Go, Rust, Java, C#, C, C++, Ruby, Kotlin, Swift, PHP, Dart — via tree-sitter native bindings (WASM fallback for the web surface). |
+| **Embedded storage, graph-default** | `@ladybugdb/core` graph engine for the structural store (default at v1) with DuckDB + `hnsw_acorn` (filter-aware HNSW via ACORN-1 + RaBitQ) + `fts` (BM25) for the temporal + retrieval views. Embedded files. No daemon. No database to operate. `CODEHUB_STORE=duck` reverts to the legacy single-file layout. |
+| **15 languages at GA** | TypeScript, JavaScript, Python, Go, Rust, Java, C#, C, C++, Ruby, Kotlin, Swift, PHP, Dart, COBOL — tree-sitter for the first 14 plus a regex provider for fixed-format COBOL. |
+| **WASM-default parse runtime** | `web-tree-sitter` WASM is the default on Node 22 and Node 24; the native `tree-sitter` N-API addon is opt-in via `OCH_NATIVE_PARSER=1` for Node 22 dev boxes. The complexity phase still uses native where supported and degrades with a one-shot warning otherwise. |
 
 ## Quick start
 
-**Requirements:** macOS, Linux, or Windows; Node 20+; pnpm 10+; Python
-3.12 (for the eval harness); `mise` recommended to manage them.
+**Requirements:** macOS, Linux, or Windows; Node 22 or 24 (Node 22
+recommended for the native-parser opt-in); pnpm 10+; Python 3.12 (only
+needed when running the SCIP indexers for Python-heavy repos);
+`mise` recommended to manage them.
 
 ```bash
 git clone https://github.com/theagenticguy/opencodehub
@@ -106,7 +109,7 @@ codehub analyze
 # your agent can now call impact, query, context, detect_changes, rename, ...
 ```
 
-## MCP tool surface (28 tools)
+## MCP tool surface (29 tools)
 
 | Tool | Purpose |
 |---|---|
@@ -116,9 +119,10 @@ codehub analyze
 | `detect_changes` | Git-diff impact — what do your current changes affect |
 | `rename` | Multi-file coordinated rename with confidence-tagged edits |
 | `route_map` / `api_impact` / `shape_check` / `tool_map` | HTTP route & MCP tool intelligence |
-| `group_query` | BM25-fused search across a group of repos |
+| `group_query` / `group_status` / `group_contracts` / `group_cross_repo_links` / `group_sync` / `group_list` | Cross-repo federation — fan out BM25, contracts, and staleness across a named group |
 | `list_repos` · `sql` | Registry & escape-hatch SQL (read-only, timeout-guarded) |
-| …and 17 more | Communities, processes, SBOM, SARIF, verdict, etc. |
+| `pack_codebase` | Deterministic Repomix-compatible code pack export |
+| …and the rest | `verdict`, `risk_trends`, `project_profile`, `dependencies`, `license_audit`, `owners`, `list_findings`, `list_findings_delta`, `list_dead_code`, `remove_dead_code`, `scan` |
 
 Architecture decision records live in [`docs/adr/`](./docs/adr/). A
 Claude Code plugin at `plugins/opencodehub/` wraps the MCP tools into
@@ -126,24 +130,32 @@ slash commands + skills — install via `codehub init`.
 
 ## Repository layout
 
-The monorepo is organised as 14 workspace packages under `packages/`:
+The monorepo is organised as 17 workspace packages under `packages/`:
 
 | Package | Purpose |
 |---|---|
 | `analysis` | Heuristic + SCIP call-graph resolution, community + flow detection |
-| `cli` | `codehub` command — `init`, `analyze`, `status`, `setup`, scanners |
-| `core-types` | Shared TypeScript types, Zod schemas, error codes |
-| `embedder` | Embedding backends — local ONNX, HTTP, SageMaker |
-| `eval` | Retrieval / graph-quality evaluation harness |
-| `gym` | Per-language F1 regression gym with SCIP baselines |
-| `ingestion` | Tree-sitter parsers, symbol extraction, import resolution |
-| `mcp` | Model Context Protocol server — 28 tools, resources |
+| `cli` | `codehub` command — `init`, `analyze`, `status`, `setup`, scanners, group federation |
+| `cobol-proleap` | ProLeap-backed deep-parse path for free-format COBOL (regex provider handles fixed-format) |
+| `core-types` | Shared TypeScript types, Zod schemas, error codes, canonical `LanguageId` and node/edge kinds |
+| `embedder` | Embedding backends — local ONNX, HTTP, SageMaker; deterministic `embedderId` fingerprint |
+| `frameworks` | HTTP route + MCP tool detectors used by `route_map` / `api_impact` / `tool_map` |
+| `ingestion` | Tree-sitter + WASM parsers, symbol extraction, import resolution, complexity phase |
+| `mcp` | Model Context Protocol server — 29 tools, resources, structured error envelopes |
+| `pack` | Deterministic Repomix-compatible code-pack generator (M5) |
+| `policy` | Allowlist + license-tier policy engine driving `license_audit` and CI gates |
 | `sarif` | SARIF schema validation and scanner output normalisation |
-| `scanners` | Subprocess wrappers for OSV, Semgrep, hadolint, tflint, etc. |
-| `scip-ingest` | SCIP indexer runners (TS, Python, Go, Rust, Java) |
+| `scanners` | Subprocess wrappers for 20 scanners — OSV, Semgrep, hadolint, tflint, detect-secrets, and the rest |
+| `scip-ingest` | SCIP indexer runners (TS, Python, Go, Rust, Java) — emits CALLS, REFERENCES, IMPLEMENTS, TYPE_OF |
 | `search` | Hybrid BM25 + HNSW (ACORN-1 + RaBitQ) query layer |
-| `storage` | DuckDB-backed graph store, deterministic `graphHash` |
+| `storage` | `IGraphStore` / `ITemporalStore` adapters — `@ladybugdb/core` (default) and DuckDB; deterministic `graphHash` |
 | `summarizer` | Process + cluster summaries for MCP responses |
+| `wiki` | LLM-narrated module pages emitted by `codehub wiki --llm` |
+
+The retrieval / graph-quality evaluation harness and the per-language F1
+regression gym used to live here as `eval` and `gym`; they were
+extracted into a sibling testbed in M5 so the production package set
+ships free of test-time dependencies.
 
 ## Embedding backends
 
@@ -199,19 +211,41 @@ for the M3 phase-1 rationale and
 [`docs/adr/0013-m7-default-flip-and-abstraction.md`](./docs/adr/0013-m7-default-flip-and-abstraction.md)
 for the M7 default-flip + interface segregation.
 
+## Parse runtime — WASM default, native opt-in
+
+`@opencodehub/ingestion` defaults to the `web-tree-sitter` (WASM)
+runtime on Node 22 and Node 24. The native `tree-sitter` N-API addon
+is opt-in on Node 22 dev boxes via `OCH_NATIVE_PARSER=1` (or
+`--native-parser` on the `codehub` CLI). Native is not supported on
+Node 24 until `node-tree-sitter@0.25.1` lands on npm
+([tree-sitter/node-tree-sitter#276](https://github.com/tree-sitter/node-tree-sitter/issues/276)).
+
+Kotlin, Swift, and Dart use `.wasm` blobs vendored at
+`packages/ingestion/vendor/wasms/` and rebuilt via
+`bash scripts/build-vendor-wasms.sh` whenever the underlying grammar
+versions in `package.json` change. The complexity phase
+(cyclomatic-complexity metrics) still uses native tree-sitter where
+available; on Node 24 or Node 22 without the opt-in, complexity
+extraction degrades with a one-shot stderr warning and all other
+parsing continues via WASM.
+
+See [`docs/adr/0013-parse-runtime-wasm-default.md`](./docs/adr/0013-parse-runtime-wasm-default.md)
+for the WASM-default rationale and the Node 24 unblock plan.
+
 ## Status
 
-**v0.1.0 — initial public release.** The codebase is feature-complete
-along the scope described below, but the project is brand-new on
-GitHub and the API surface is not yet stable.
+**v1 — feature-complete on M1–M7.** Tracks A (M7 graph-DB default + the
+`IGraphStore` / `ITemporalStore` interface segregation), B (20-scanner
+fleet incl. detect-secrets), C (debt sweep — embedder fingerprint, SCIP
+REFERENCES + TYPE_OF), and D (dogfood polish) have all merged. The
+current shipped tag remains `0.1.1`; `1.0.0` is cut once schema +
+tool-surface stability is signed off.
 
 While on `0.x`, **any release may contain breaking changes** to the
 graph schema, MCP tool shapes, CLI flags, or storage layout. Breaking
 changes are called out with `!` or a `BREAKING CHANGE:` footer in the
 commit log and summarised in each release's generated CHANGELOG.
 
-`1.0.0` will be cut when we commit to schema + tool-surface stability.
-
 ## Supply-chain posture
 
 - **CycloneDX SBOM** at [`SBOM.cdx.json`](./SBOM.cdx.json) (regenerated on every release)

From 69eac8f8bb2f95546cbbc05490c95a7a5d738519 Mon Sep 17 00:00:00 2001
From: Laith Al-Saadoon <alsaadoonlaith@gmail.com>
Date: Sun, 10 May 2026 16:36:28 +0000
Subject: [PATCH 08/10] docs(docs): cross-link superseded ADRs and confirm
 storage/parse defaults

- Flip ADR 0011 (LadybugDB phase-1) status from "Proposed" to "Accepted"
  -- M3 has merged. Add a forward link to ADR 0013 (M7 phase-2).
- Flip ADR 0013-m7 (default-flip + interface segregation) status to
  "Accepted" -- the Track A PR has merged.
- Cross-link the two ADR 0013 files (m7 default-flip + parse-runtime
  WASM default) -- both numbers landed concurrently on the same release;
  the next ADR uses 0014.
- Scrub session-local spec coordinates from ADR text so the docs read
  as durable architecture rationale, not work-tracking artefacts. The
  underlying decisions and code paths remain.
---
 docs/adr/0011-graph-db-backend.md             |  5 +-
 .../0013-m7-default-flip-and-abstraction.md   | 63 ++++++++++---------
 docs/adr/0013-parse-runtime-wasm-default.md   |  5 ++
 ...cip-references-and-embedder-fingerprint.md | 33 +++++-----
 4 files changed, 60 insertions(+), 46 deletions(-)

diff --git a/docs/adr/0011-graph-db-backend.md b/docs/adr/0011-graph-db-backend.md
index 59b129c6..ff7ebfcc 100644
--- a/docs/adr/0011-graph-db-backend.md
+++ b/docs/adr/0011-graph-db-backend.md
@@ -1,11 +1,14 @@
 # ADR 0011 — Graph-DB backend (LadybugDB phase-1)
 
-- Status: **Proposed** — 2026-05-05 (flips to **Accepted** on the M3 merge).
+- Status: **Accepted** — 2026-05-05 (Proposed) → flipped on the M3 merge.
 - Authors: Laith Al-Saadoon + Claude.
 - Branch: `feat/v1-m3-m4`.
 - Supersedes nothing. Interacts with ADR 0001 (DuckDB backend stays the
   default through M6; this ADR records the opt-in second backend and the
   phased plan to flip the default in M7).
+- Followed by ADR 0013 (M7 default-flip + interface segregation), which
+  records the M7 flip from "DuckDB-default + LadybugDB opt-in" to
+  "LadybugDB-default with auto-fallback to DuckDB".
 
 ## Context
 
diff --git a/docs/adr/0013-m7-default-flip-and-abstraction.md b/docs/adr/0013-m7-default-flip-and-abstraction.md
index 278c1d88..29696e87 100644
--- a/docs/adr/0013-m7-default-flip-and-abstraction.md
+++ b/docs/adr/0013-m7-default-flip-and-abstraction.md
@@ -1,7 +1,12 @@
 # ADR 0013 — M7 default-flip + storage abstraction (LadybugDB phase-2)
 
-- Status: **Proposed** — 2026-05-09 (flips to **Accepted** on the
-  `feat/v1-finalize-track-a` merge).
+> Note: there is a sibling ADR — `0013-parse-runtime-wasm-default.md` —
+> that landed concurrently and shares the same number. Both are kept
+> in-tree because they were authored in parallel branches and accepted
+> on the same release. The next ADR uses 0014.
+
+- Status: **Accepted** — 2026-05-09 (Proposed) → flipped on the
+  `feat/v1-finalize-track-a` merge (PR #71).
 - Authors: Laith Al-Saadoon + Claude.
 - Branch: `feat/v1-finalize-track-a`.
 - Supersedes nothing. Extends ADR 0011 (LadybugDB phase-1) by flipping
@@ -87,7 +92,7 @@ promise. The probe never blocks synchronously and never re-runs.
 
 Track A landed three structural changes that this ADR records.
 
-### Split `IGraphStore` into graph-only + `ITemporalStore` (AC-A-1)
+### Split `IGraphStore` into graph-only + `ITemporalStore`
 
 `packages/storage/src/interface.ts` now exports two interfaces:
 
@@ -105,16 +110,16 @@ interfaces structurally and is returned twice (one connection serves
 both). For the `lbug` backend a `GraphDbStore` backs `graph` and a
 sibling `DuckDbStore` backs `temporal`.
 
-### Hoisted column encoders + sentinel coercions (AC-A-2)
+### Hoisted column encoders + sentinel coercions
 
 `packages/storage/src/column-encode.ts` carries the per-column
 serialization rules previously duplicated in
 `duckdb-adapter.ts:bulkLoad` and `graphdb-adapter.ts:bulkLoad`. The
 hoist resolves the `step: 0` vs `step: null` parity asymmetry (ADR
-0011 §graphHash invariant captured the workaround; AC-A-2 makes it a
-shared encoder so both adapters cannot drift).
+0011 §graphHash invariant captured the workaround; the shared encoder
+prevents the two adapters from drifting).
 
-### Public-interface parity harness + community-adapter conformance suite (AC-A-7, AC-A-11)
+### Public-interface parity harness + community-adapter conformance suite
 
 `packages/storage/src/test-utils/parity-harness.ts` exports
 `rebuildFromStore(graph: IGraphStore): Promise<KnowledgeGraph>` and
@@ -156,25 +161,25 @@ The 2 specialized finders are `loadXrefs(opts)` and
 `loadSkeleton(opts)` — both compose multiple typed finders behind a
 single call to keep the pack layer's I/O contract narrow.
 
-## 108-site SQL migration (AC-A-6 a/b/c/d)
+## 108-site SQL migration
 
 The migration landed in four sub-commits, sequenced sequentially to
 keep each commit reviewable:
 
-| Sub-commit | Package | Sites |
-|---|---|---|
-| AC-A-6a | `analysis/` | 27 |
-| AC-A-6b | `mcp/` | 46 |
-| AC-A-6c | `pack/` + `wiki/` | 15 |
-| AC-A-6d | `cli/` | 20 |
+| Package | Sites |
+|---|---|
+| `analysis/` | 27 |
+| `mcp/` | 46 |
+| `pack/` + `wiki/` | 15 |
+| `cli/` | 20 |
 
 Total: **108 raw-SQL call sites** replaced with typed-finder calls.
 Every migrated tool runs end-to-end on BOTH DuckDb and LadybugDB
 backends (the parity harness is wired into every consumer test).
 `packages/analysis/src/test-utils.ts` was rewritten from a
 DuckDB-dialect regex fake into a typed `IGraphStore` fake that
-implements the finder surface (AC-A-6 sub-task), unblocking the rest
-of the consumer-side migration.
+implements the finder surface, unblocking the rest of the
+consumer-side migration.
 
 ## Dual-artifact detection
 
@@ -203,8 +208,8 @@ identifiers are reserved for out-of-tree adapter packages. The escape
 hatch is:
 
 - A community adapter implements `IGraphStore` directly. The
-  conformance suite (AC-A-11) is the contract: pass it, claim
-  conformance.
+  conformance suite (`packages/storage/src/test-utils/conformance.ts`)
+  is the contract: pass it, claim conformance.
 - The optional `execCypher?(query, params?, opts?)` hook on
   `IGraphStore` lets adapters with a Cypher-native query path expose
   it for the `sql` MCP tool's `cypher` input mode without leaking
@@ -290,20 +295,15 @@ of `@opencodehub/storage` required.
 
 ## Status
 
-- **Proposed**: 2026-05-09 (Track A AC-A-9 commit).
+- **Proposed**: 2026-05-09 (Track A authoring commit).
 - **Accepted**: on merge of `feat/v1-finalize-track-a` → `main` (the PR
-  that ships AC-A-9 alongside AC-A-1 through AC-A-11).
+  that shipped this ADR alongside the rest of Track A's deliverables).
 - **Superseded**: not on the v1.0 roadmap. M8+ may add new edge kinds
   or community-backend extension points; those changes get follow-up
   ADRs.
 
 ## References
 
-- Spec: `.erpaval/specs/006-v1-finalize/architecture-revised.md`
-  §AC-A-1 (interface split), §AC-A-2 (column encoders), §AC-A-3
-  (`ITemporalStore` route), §AC-A-6 (108-SQL migration), §AC-A-7
-  (parity harness), §AC-A-8 (`describeArtifacts`), §AC-A-9 (this ADR
-  + the default flip), §AC-A-11 (conformance suite).
 - Code:
   - `packages/storage/src/interface.ts` — `IGraphStore` + `ITemporalStore`
     type definitions; the typed-finder method surface.
@@ -322,7 +322,8 @@ of `@opencodehub/storage` required.
   - `packages/storage/src/resolver.test.ts` — async resolver +
     dual-artifact detection.
   - `packages/storage/src/graph-hash-parity.test.ts` — graph-hash
-    parity gate (continues to enforce ADR 0011's W-M3-1).
+    parity gate (continues to enforce ADR 0011's byte-identity
+    invariant).
   - `packages/storage/src/temporal-parity.test.ts` — round-trip
     parity for `ITemporalStore` adapters.
   - `packages/storage/src/interface.test.ts` — interface-level
@@ -334,7 +335,7 @@ of `@opencodehub/storage` required.
   - ADR 0011 — LadybugDB phase-1. This ADR is its M7 follow-up.
   - ADR 0012 — Repo as a first-class graph node. The M6 federation
     surface routes through the new typed finders via this ADR's
-    AC-A-6 migration.
+    108-site SQL migration.
 
 ## Provenance
 
@@ -356,15 +357,15 @@ checksums because the two artifacts are written by different engines
 and have different on-disk representations. mtime is the only stable
 signal.
 
-## Empirical evidence — graphHash parity audit (AC-A-10)
+## Empirical evidence — graphHash parity audit
 
 The whole-pipeline parity gate is `scripts/m7-parity-audit.sh`. It runs
 `codehub analyze --force` against the same corpus under
 `CODEHUB_STORE=duck` and `CODEHUB_STORE=lbug`, then compares the
 `graph <hash>` summary line emitted by each invocation. This is the
-end-to-end companion to the in-memory `assertGraphParity` harness
-(AC-A-7); together they pin U1 (graphHash byte-identity) from both
-layers — fixtures and a real on-disk analyze.
+end-to-end companion to the in-memory `assertGraphParity` harness;
+together they pin graphHash byte-identity from both layers — fixtures
+and a real on-disk analyze.
 
 The script is wired into `scripts/acceptance.sh` as gate 17 (the final
 gate). Sample outputs follow.
diff --git a/docs/adr/0013-parse-runtime-wasm-default.md b/docs/adr/0013-parse-runtime-wasm-default.md
index 35fa5f67..0aa009c2 100644
--- a/docs/adr/0013-parse-runtime-wasm-default.md
+++ b/docs/adr/0013-parse-runtime-wasm-default.md
@@ -1,5 +1,10 @@
 # ADR 0013 — Parse runtime: WASM default, native opt-in
 
+> Note: there is a sibling ADR — `0013-m7-default-flip-and-abstraction.md`
+> — that landed concurrently and shares the same number. Both are kept
+> in-tree because they were authored in parallel branches and accepted
+> on the same release. The next ADR uses 0014.
+
 - Status: **Accepted** — 2026-05-08.
 - Authors: Laith Al-Saadoon + Claude.
 - Branch: `feat/node24-wasm-default`.
diff --git a/docs/adr/0014-scip-references-and-embedder-fingerprint.md b/docs/adr/0014-scip-references-and-embedder-fingerprint.md
index 7c6c2d27..3854c363 100644
--- a/docs/adr/0014-scip-references-and-embedder-fingerprint.md
+++ b/docs/adr/0014-scip-references-and-embedder-fingerprint.md
@@ -7,9 +7,9 @@
 
 ## Context
 
-Two unrelated holes in v1.0 finalize, both routing through a shared one-time graphHash content delta. They land in a single ADR per spec.md§Q7 because the fixture-regeneration cost is paid once.
+Two unrelated holes in v1.0 finalize, both routing through a shared one-time graphHash content delta. They land in a single ADR because the fixture-regeneration cost is paid once.
 
-### Hole A — Embedder rebuild-on-switch silent corruption (AC-C-3)
+### Hole A — Embedder rebuild-on-switch silent corruption
 
 The `embeddings` table on disk is populated by ONE specific embedder at index time. The currently-shipped store_meta schema (`packages/storage/src/schema-ddl.ts:172-183`) records `schema_version, last_commit, indexed_at, node_count, edge_count, stats_json, cache_hit_ratio, cache_size_bytes, last_compaction` — but NOT which embedder produced the vectors.
 
@@ -17,7 +17,7 @@ Failure mode: an operator runs `codehub analyze` with the local ONNX `gte-modern
 
 There is no test suite that catches this; there is no error envelope at the query path.
 
-### Hole B — SCIP REFERENCES + TYPE_OF unwired (AC-C-5)
+### Hole B — SCIP REFERENCES + TYPE_OF unwired
 
 `packages/scip-ingest/src/derive.ts` already correctly:
 - Emits CALLS edges via `deriveEdges` for function-like SCIP occurrences (`derive.ts:128-152`).
@@ -39,9 +39,9 @@ The combined effect: every existing OCH index understates the call/reference gra
 3. `Store.getMeta()` returns the persisted value via the new `StoreMeta.embedderModelId?: string` field.
 4. At query time (cli `runQuery`, MCP `runQuery`), read `meta.embedderModelId`, compare to `embedder.modelId`:
    - Equal → proceed.
-   - Persisted is `undefined` (pre-AC-C-3 store) → proceed; the operator is trusted to know what they indexed.
+   - Persisted is `undefined` (store written before this ADR) → proceed; the operator is trusted to know what they indexed.
    - Mismatch + force flag set → proceed.
-   - Mismatch + no force flag → refuse. CLI prints to stderr and `process.exit(2)` per E-C-3. MCP returns a `EMBEDDER_MISMATCH` envelope via `toolError` per the same hint string.
+   - Mismatch + no force flag → refuse. CLI prints to stderr and `process.exit(2)`. MCP returns a `EMBEDDER_MISMATCH` envelope via `toolError` using the same hint string.
 5. Frozen remediation hint string lives in `packages/embedder/src/fingerprint.ts` as `EMBEDDER_MISMATCH_HINT`. Both surfaces import it so the message can never drift.
 6. CLI `--force-backend-mismatch` flag and MCP `force_backend_mismatch` tool input give the operator an override path. Default `false`.
 
@@ -64,7 +64,7 @@ The `assertEmbedderCompatible(persistedModelId, currentModelId, force)` helper l
 
 ### Cross-track sequencing
 
-This ADR is shared with AC-C-3 (Hole A) and AC-C-5 (Hole B). They land in the same Track C PR; the fixture regen runs once for both.
+Hole A and Hole B land in the same Track C PR; the fixture regen runs once for both.
 
 ### Migration cost
 
@@ -84,8 +84,8 @@ For Hole B, every existing store needs a `codehub analyze --force` to pick up th
 - **Force re-index on EVERY embedder env-var change.** Too aggressive for SageMaker→ONNX fallbacks during dev. The override flag exists for that case.
 
 ### Hole B
-- **Insert TYPE_OF mid-union next to IMPLEMENTS.** Violates W-A-2 + the `edges.ts:29-32` append-only comment. Would break every existing graphHash on every existing OCH index, even for content with no IMPLEMENTS / TYPE_OF / REFERENCES. Rejected.
-- **Split AC-C-5 into a sibling PR after Track C.** Considered in `pr-split-analysis.md` Option (b). Rejected because the fixture-regeneration cost would be paid twice (once for the v1.0 finalize hash bump that ships SCIP REFERENCES, once for the next ADR adding TYPE_OF). Bundling them is cheaper.
+- **Insert TYPE_OF mid-union next to IMPLEMENTS.** Violates the `edges.ts:29-32` append-only comment. Would break every existing graphHash on every existing OCH index, even for content with no IMPLEMENTS / TYPE_OF / REFERENCES. Rejected.
+- **Split Hole B into a sibling PR after Track C.** Considered and rejected because the fixture-regeneration cost would be paid twice (once for the v1.0 finalize hash bump that ships SCIP REFERENCES, once for the next ADR adding TYPE_OF). Bundling them is cheaper.
 
 ## Validation
 
@@ -98,9 +98,14 @@ For Hole B, every existing store needs a `codehub analyze --force` to pick up th
 
 ## References
 
-- `.erpaval/specs/006-v1-finalize/spec.md§AC-C-3, §AC-C-5, §E-C-3, §E-C-4, §W-A-2`
-- `.erpaval/sessions/session-33f24f/research-detectsecrets-scip.yaml` (SCIP role enum + Relationship message)
-- `.erpaval/solutions/architecture-patterns/scip-callee-definition-site.md`
-- `.erpaval/solutions/conventions/scip-0-indexed-vs-graph-1-indexed.md`
-- `docs/adr/0011-graph-db-backend.md` (M3+M6 IGraphStore precedent)
-- `docs/adr/0013-m7-default-flip-and-abstraction.md` (M7 LadybugDB default flip)
+- `packages/embedder/src/fingerprint.ts` — `assertEmbedderCompatible`,
+  the frozen `EMBEDDER_MISMATCH_HINT` string.
+- `packages/scip-ingest/src/derive.ts` — REFERENCES emission and the
+  `is_implementation`/`is_type_definition` collector.
+- `packages/ingestion/src/pipeline/phases/scip-index.ts` — `emitEdges`
+  and the new `emitRelations` sibling.
+- `packages/core-types/src/edges.ts` — append-only `RelationType`
+  union; `TYPE_OF` lands at position 25.
+- `docs/adr/0011-graph-db-backend.md` — `IGraphStore` precedent.
+- `docs/adr/0013-m7-default-flip-and-abstraction.md` — M7 LadybugDB
+  default flip.

From edb362e0af71ca581fe45d09c12465c28626e4a0 Mon Sep 17 00:00:00 2001
From: Laith Al-Saadoon <alsaadoonlaith@gmail.com>
Date: Sun, 10 May 2026 16:36:40 +0000
Subject: [PATCH 09/10] =?UTF-8?q?docs(repo):=20CHANGELOG=20+=20USECASE=20+?=
 =?UTF-8?q?=20AGENTS=20=E2=80=94=20sync=20with=20v1=20reality?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

- CHANGELOG: add an [Unreleased] block summarizing this PR's bug sweep
  (cli/scan SARIF ingest, cli/doctor binding resolution, smoke-mcp
  29-tool assertion) and docs refresh.
- AGENTS: bump 28 -> 29 tools; drop session-local spec coordinates from
  the AMBIGUOUS_REPO worked example so AGENTS.md reads cleanly as a
  contributor reference (CLAUDE.md keeps the original prose for now).
- OBJECTIVES: bump 28 -> 29 tools, 14 -> 15 GA languages, note that the
  retrieval / F1 gym is now a sibling testbed.
---
 AGENTS.md     | 18 ++++++++++--------
 CHANGELOG.md  | 19 +++++++++++++++++++
 OBJECTIVES.md | 19 ++++++++++---------
 3 files changed, 39 insertions(+), 17 deletions(-)

diff --git a/AGENTS.md b/AGENTS.md
index c15fe43d..1d1666f7 100644
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -1,4 +1,7 @@
-<!-- Intentionally synchronized with CLAUDE.md. Edit both files together. -->
+<!-- Intentionally synchronized with CLAUDE.md. Edit both files together.
+     v1 docs sweep: AGENTS.md drops session-local spec coordinates that
+     CLAUDE.md still carries. The substantive guidance is identical. -->
+
 ## OpenCodeHub MCP Tools
 
 This repository has been indexed by OpenCodeHub. When you are working in this
@@ -19,7 +22,7 @@ with the working tree. `codehub status` reports staleness.
 
 ## Full MCP surface
 
-The full MCP surface is **28 tools** (see `packages/mcp/src/server.ts`);
+The full MCP surface is **29 tools** (see `packages/mcp/src/server.ts`);
 the 7 listed above are the high-frequency exploration tools. For the
 full inventory, use the `/opencodehub-guide` skill.
 
@@ -37,12 +40,11 @@ the list was truncated.
 
 See ADR 0012 (`docs/adr/0012-repo-as-first-class-node.md`) for the
 rationale behind `repo_uri` as a first-class node attribute. The
-`repo_uri` shape was promoted to a typed graph attribute by AC-M6-1
-(`packages/core-types/src/nodes.ts:524-552`). `group_cross_repo_links`
-(the AC-M6-3-reframed MCP tool) and the `group_*` family (AC-M6-4) all
-emit `repo_uri` in the same canonical form, so a caller can use any of
-those tools' `repo_uri` outputs as input to `AMBIGUOUS_REPO.choices`
-retries.
+`repo_uri` shape is a typed graph attribute on every `Repo` node
+(`packages/core-types/src/nodes.ts`). `group_cross_repo_links` and
+the `group_*` family of MCP tools all emit `repo_uri` in the same
+canonical form, so a caller can use any of those tools' `repo_uri`
+outputs as input to `AMBIGUOUS_REPO.choices` retries.
 
 Worked example — error envelope, then retry:
 
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 14555a35..9f61e08a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,24 @@
 # Changelog
 
+## [Unreleased]
+
+### Fixed
+
+- **cli:** `scan` ingests SARIF into the scanned repo, not CWD.
+- **cli:** `doctor` resolves native bindings from owner workspaces.
+- **smoke-mcp:** asserts 29 tools, matching the v1.0 server surface.
+
+### Docs
+
+- **repo:** README v1.0 status, 29-tool surface, parse-runtime section,
+  and accurate 17-package list (drops `eval` / `gym`, adds
+  `cobol-proleap`, `frameworks`, `pack`, `policy`, `wiki`).
+- **adr:** cross-link the two concurrently-numbered ADR 0013 files,
+  flip 0011 + 0013-m7 status to Accepted, and scrub session-local
+  spec coordinates from ADR text.
+- **repo:** sync `CHANGELOG`, `USECASE`, `AGENTS`, and `OBJECTIVES`
+  with v1 reality (tool count, language count, package set).
+
 ## [0.1.1](https://github.com/theagenticguy/opencodehub/compare/root-v0.1.0...root-v0.1.1) (2026-04-22)
 
 
diff --git a/OBJECTIVES.md b/OBJECTIVES.md
index 5f7d9ec9..6118a9dc 100644
--- a/OBJECTIVES.md
+++ b/OBJECTIVES.md
@@ -10,7 +10,7 @@ scope.
    call.** *Because the README's problem statement is exactly this:
    grep is textual, language servers are per-file, embeddings are
    lossy; agents need callers, callees, processes, and blast radius
-   answered before they write a diff, and the 28-tool MCP surface is
+   answered before they write a diff, and the 29-tool MCP surface is
    the primary product.*
 
 2. **Stay Apache-2.0 end-to-end, with every transitive runtime
@@ -26,21 +26,22 @@ scope.
    commit, and `scripts/acceptance.sh` gate 6 gates on exactly that
    invariant.*
 
-4. **Cover the 14 GA languages with tree-sitter and upgrade five of
-   them (TypeScript, Python, Go, Rust, Java) with SCIP indexers.**
+4. **Cover the 15 GA languages (14 via tree-sitter plus a regex
+   provider for fixed-format COBOL) and upgrade five of them
+   (TypeScript, Python, Go, Rust, Java) with SCIP indexers.**
    *Because heuristic call-graph edges miss cross-module resolution,
    the `scip-index` phase runs each language's native SCIP indexer
    once, the `confidence-demote` phase reconciles heuristic and
-   compiler-grade edges, and the gym harness gates per-language F1
-   with SCIP-derived baselines.*
+   compiler-grade edges, and the gym harness (extracted to a sibling
+   testbed in M5) gates per-language F1 with SCIP-derived baselines.*
 
 ## Quality bar
 
 5. **Hold a three-layer regression gate on every eval and gym run.**
-   *Because the gym's absolute-F1-floor + relative-F1-delta + per-case
-   non-regression layering is baked into the harness, and acceptance
-   gate 9 requires ≥ 40/49 Python-eval cases to pass — soft regressions
-   are not an option.*
+   *Because the sibling testbed's absolute-F1-floor + relative-F1-delta
+   + per-case non-regression layering is baked into the harness, and
+   acceptance gate 9 requires ≥ 40/49 Python-eval cases to pass — soft
+   regressions are not an option.*
 
 6. **Fail CI on any non-zero exit.** *Because `pnpm run check` chains
    lint → typecheck → test → banned-strings and exits on first

From e186aea1af61ae38661c7008788ecb0a115f8cc7 Mon Sep 17 00:00:00 2001
From: Laith Al-Saadoon <alsaadoonlaith@gmail.com>
Date: Sun, 10 May 2026 16:38:58 +0000
Subject: [PATCH 10/10] docs(docs): restore ADR-permanent spec coordinates per
 PR #74 policy

PR #74 (`f09d804`) explicitly carved out `docs/adr/*` as the place
where ERPAVal spec coordinates ARE allowed: "ADR text and docs/adr/*
files retain coordinates where they cite the permanent decision
rationale". Commit 69eac8f over-scrubbed those references.

Restored:
- ADR 0013-m7: AC-A-1 / AC-A-2 / AC-A-6 (a-d) / AC-A-7 / AC-A-9 /
  AC-A-11 in section headers + body, the four-row sub-commit table
  with sub-commit IDs, the W-M3-1 byte-identity invariant citation,
  and the architecture-revised.md spec-cross-link block.
- ADR 0014: AC-C-3, AC-C-5, E-C-3, W-A-2 in section headers, hint
  strings, and the alternatives section.

Kept from 69eac8f:
- ADR 0011 + 0013-m7 status flips (Proposed -> Accepted) since both
  PRs have merged.
- Sibling-ADR cross-link banner on the duplicate 0013 collision.
- ADR 0014 References block stays as code paths (the gitignored
  .erpaval/specs/... and .erpaval/sessions/... entries rot once the
  packet graduates -- swap is per the no-spec-coordinate-leakage
  durable lesson, with code paths as the durable substitute).
---
 .../0013-m7-default-flip-and-abstraction.md   | 44 ++++++++++---------
 ...cip-references-and-embedder-fingerprint.md | 16 +++----
 2 files changed, 32 insertions(+), 28 deletions(-)

diff --git a/docs/adr/0013-m7-default-flip-and-abstraction.md b/docs/adr/0013-m7-default-flip-and-abstraction.md
index 29696e87..8affdae5 100644
--- a/docs/adr/0013-m7-default-flip-and-abstraction.md
+++ b/docs/adr/0013-m7-default-flip-and-abstraction.md
@@ -92,7 +92,7 @@ promise. The probe never blocks synchronously and never re-runs.
 
 Track A landed three structural changes that this ADR records.
 
-### Split `IGraphStore` into graph-only + `ITemporalStore`
+### Split `IGraphStore` into graph-only + `ITemporalStore` (AC-A-1)
 
 `packages/storage/src/interface.ts` now exports two interfaces:
 
@@ -110,16 +110,16 @@ interfaces structurally and is returned twice (one connection serves
 both). For the `lbug` backend a `GraphDbStore` backs `graph` and a
 sibling `DuckDbStore` backs `temporal`.
 
-### Hoisted column encoders + sentinel coercions
+### Hoisted column encoders + sentinel coercions (AC-A-2)
 
 `packages/storage/src/column-encode.ts` carries the per-column
 serialization rules previously duplicated in
 `duckdb-adapter.ts:bulkLoad` and `graphdb-adapter.ts:bulkLoad`. The
 hoist resolves the `step: 0` vs `step: null` parity asymmetry (ADR
-0011 §graphHash invariant captured the workaround; the shared encoder
-prevents the two adapters from drifting).
+0011 §graphHash invariant captured the workaround; AC-A-2 makes it a
+shared encoder so both adapters cannot drift).
 
-### Public-interface parity harness + community-adapter conformance suite
+### Public-interface parity harness + community-adapter conformance suite (AC-A-7, AC-A-11)
 
 `packages/storage/src/test-utils/parity-harness.ts` exports
 `rebuildFromStore(graph: IGraphStore): Promise<KnowledgeGraph>` and
@@ -161,25 +161,25 @@ The 2 specialized finders are `loadXrefs(opts)` and
 `loadSkeleton(opts)` — both compose multiple typed finders behind a
 single call to keep the pack layer's I/O contract narrow.
 
-## 108-site SQL migration
+## 108-site SQL migration (AC-A-6 a/b/c/d)
 
 The migration landed in four sub-commits, sequenced sequentially to
 keep each commit reviewable:
 
-| Package | Sites |
-|---|---|
-| `analysis/` | 27 |
-| `mcp/` | 46 |
-| `pack/` + `wiki/` | 15 |
-| `cli/` | 20 |
+| Sub-commit | Package | Sites |
+|---|---|---|
+| AC-A-6a | `analysis/` | 27 |
+| AC-A-6b | `mcp/` | 46 |
+| AC-A-6c | `pack/` + `wiki/` | 15 |
+| AC-A-6d | `cli/` | 20 |
 
 Total: **108 raw-SQL call sites** replaced with typed-finder calls.
 Every migrated tool runs end-to-end on BOTH DuckDb and LadybugDB
 backends (the parity harness is wired into every consumer test).
 `packages/analysis/src/test-utils.ts` was rewritten from a
 DuckDB-dialect regex fake into a typed `IGraphStore` fake that
-implements the finder surface, unblocking the rest of the
-consumer-side migration.
+implements the finder surface (AC-A-6 sub-task), unblocking the rest
+of the consumer-side migration.
 
 ## Dual-artifact detection
 
@@ -208,8 +208,8 @@ identifiers are reserved for out-of-tree adapter packages. The escape
 hatch is:
 
 - A community adapter implements `IGraphStore` directly. The
-  conformance suite (`packages/storage/src/test-utils/conformance.ts`)
-  is the contract: pass it, claim conformance.
+  conformance suite (AC-A-11) is the contract: pass it, claim
+  conformance.
 - The optional `execCypher?(query, params?, opts?)` hook on
   `IGraphStore` lets adapters with a Cypher-native query path expose
   it for the `sql` MCP tool's `cypher` input mode without leaking
@@ -295,9 +295,9 @@ of `@opencodehub/storage` required.
 
 ## Status
 
-- **Proposed**: 2026-05-09 (Track A authoring commit).
+- **Proposed**: 2026-05-09 (Track A AC-A-9 commit).
 - **Accepted**: on merge of `feat/v1-finalize-track-a` → `main` (the PR
-  that shipped this ADR alongside the rest of Track A's deliverables).
+  that ships AC-A-9 alongside AC-A-1 through AC-A-11).
 - **Superseded**: not on the v1.0 roadmap. M8+ may add new edge kinds
   or community-backend extension points; those changes get follow-up
   ADRs.
@@ -322,13 +322,17 @@ of `@opencodehub/storage` required.
   - `packages/storage/src/resolver.test.ts` — async resolver +
     dual-artifact detection.
   - `packages/storage/src/graph-hash-parity.test.ts` — graph-hash
-    parity gate (continues to enforce ADR 0011's byte-identity
-    invariant).
+    parity gate (continues to enforce ADR 0011's W-M3-1).
   - `packages/storage/src/temporal-parity.test.ts` — round-trip
     parity for `ITemporalStore` adapters.
   - `packages/storage/src/interface.test.ts` — interface-level
     contract assertions.
   - `packages/storage/src/finders.test.ts` — typed-finder coverage.
+- Spec: `.erpaval/specs/006-v1-finalize/architecture-revised.md`
+  §AC-A-1 (interface split), §AC-A-2 (column encoders), §AC-A-3
+  (`ITemporalStore` route), §AC-A-6 (108-SQL migration), §AC-A-7
+  (parity harness), §AC-A-8 (`describeArtifacts`), §AC-A-9 (this ADR
+  + the default flip), §AC-A-11 (conformance suite).
 - Related ADRs:
   - ADR 0001 — DuckDB selection. This ADR keeps DuckDB as the
     temporal store and the legacy graph store; no rip-out.
diff --git a/docs/adr/0014-scip-references-and-embedder-fingerprint.md b/docs/adr/0014-scip-references-and-embedder-fingerprint.md
index 3854c363..869e3e3a 100644
--- a/docs/adr/0014-scip-references-and-embedder-fingerprint.md
+++ b/docs/adr/0014-scip-references-and-embedder-fingerprint.md
@@ -7,9 +7,9 @@
 
 ## Context
 
-Two unrelated holes in v1.0 finalize, both routing through a shared one-time graphHash content delta. They land in a single ADR because the fixture-regeneration cost is paid once.
+Two unrelated holes in v1.0 finalize, both routing through a shared one-time graphHash content delta. They land in a single ADR per spec.md§Q7 because the fixture-regeneration cost is paid once.
 
-### Hole A — Embedder rebuild-on-switch silent corruption
+### Hole A — Embedder rebuild-on-switch silent corruption (AC-C-3)
 
 The `embeddings` table on disk is populated by ONE specific embedder at index time. The currently-shipped store_meta schema (`packages/storage/src/schema-ddl.ts:172-183`) records `schema_version, last_commit, indexed_at, node_count, edge_count, stats_json, cache_hit_ratio, cache_size_bytes, last_compaction` — but NOT which embedder produced the vectors.
 
@@ -17,7 +17,7 @@ Failure mode: an operator runs `codehub analyze` with the local ONNX `gte-modern
 
 There is no test suite that catches this; there is no error envelope at the query path.
 
-### Hole B — SCIP REFERENCES + TYPE_OF unwired
+### Hole B — SCIP REFERENCES + TYPE_OF unwired (AC-C-5)
 
 `packages/scip-ingest/src/derive.ts` already correctly:
 - Emits CALLS edges via `deriveEdges` for function-like SCIP occurrences (`derive.ts:128-152`).
@@ -39,9 +39,9 @@ The combined effect: every existing OCH index understates the call/reference gra
 3. `Store.getMeta()` returns the persisted value via the new `StoreMeta.embedderModelId?: string` field.
 4. At query time (cli `runQuery`, MCP `runQuery`), read `meta.embedderModelId`, compare to `embedder.modelId`:
    - Equal → proceed.
-   - Persisted is `undefined` (store written before this ADR) → proceed; the operator is trusted to know what they indexed.
+   - Persisted is `undefined` (pre-AC-C-3 store) → proceed; the operator is trusted to know what they indexed.
    - Mismatch + force flag set → proceed.
-   - Mismatch + no force flag → refuse. CLI prints to stderr and `process.exit(2)`. MCP returns a `EMBEDDER_MISMATCH` envelope via `toolError` using the same hint string.
+   - Mismatch + no force flag → refuse. CLI prints to stderr and `process.exit(2)` per E-C-3. MCP returns a `EMBEDDER_MISMATCH` envelope via `toolError` per the same hint string.
 5. Frozen remediation hint string lives in `packages/embedder/src/fingerprint.ts` as `EMBEDDER_MISMATCH_HINT`. Both surfaces import it so the message can never drift.
 6. CLI `--force-backend-mismatch` flag and MCP `force_backend_mismatch` tool input give the operator an override path. Default `false`.
 
@@ -64,7 +64,7 @@ The `assertEmbedderCompatible(persistedModelId, currentModelId, force)` helper l
 
 ### Cross-track sequencing
 
-Hole A and Hole B land in the same Track C PR; the fixture regen runs once for both.
+This ADR is shared with AC-C-3 (Hole A) and AC-C-5 (Hole B). They land in the same Track C PR; the fixture regen runs once for both.
 
 ### Migration cost
 
@@ -84,8 +84,8 @@ For Hole B, every existing store needs a `codehub analyze --force` to pick up th
 - **Force re-index on EVERY embedder env-var change.** Too aggressive for SageMaker→ONNX fallbacks during dev. The override flag exists for that case.
 
 ### Hole B
-- **Insert TYPE_OF mid-union next to IMPLEMENTS.** Violates the `edges.ts:29-32` append-only comment. Would break every existing graphHash on every existing OCH index, even for content with no IMPLEMENTS / TYPE_OF / REFERENCES. Rejected.
-- **Split Hole B into a sibling PR after Track C.** Considered and rejected because the fixture-regeneration cost would be paid twice (once for the v1.0 finalize hash bump that ships SCIP REFERENCES, once for the next ADR adding TYPE_OF). Bundling them is cheaper.
+- **Insert TYPE_OF mid-union next to IMPLEMENTS.** Violates W-A-2 + the `edges.ts:29-32` append-only comment. Would break every existing graphHash on every existing OCH index, even for content with no IMPLEMENTS / TYPE_OF / REFERENCES. Rejected.
+- **Split AC-C-5 into a sibling PR after Track C.** Considered in `pr-split-analysis.md` Option (b). Rejected because the fixture-regeneration cost would be paid twice (once for the v1.0 finalize hash bump that ships SCIP REFERENCES, once for the next ADR adding TYPE_OF). Bundling them is cheaper.
 
 ## Validation