Merge working-tree manifests with staged overrides and deduplicate Prolog codec by Looted · Pull Request #139 · Looted/kibi

Looted · 2026-04-06T11:10:49Z

No description provided.

…e codec toPrologString - buildManifestLookup() now pre-populates the manifest lookup from the working-tree config.paths.symbols file before processing staged manifests. This prevents code-only staged changes from incorrectly failing traceability when symbols.yaml is not staged but is already linked in the KB. - Remove duplicate toPrologString() in temp-kb.ts and import the shared implementation from ../prolog/codec to keep Prolog serialisation consistent. - Add .changeset/fix-manifest-lookup-and-prolog-codec.md for release tracking. Agent-Logs-Url: https://github.com/Looted/kibi/sessions/d11497ec-c000-4b40-978d-2f5d5eb012e4 Co-authored-by: Looted <6255880+Looted@users.noreply.github.com>

Agent-Logs-Url: https://github.com/Looted/kibi/sessions/d11497ec-c000-4b40-978d-2f5d5eb012e4 Co-authored-by: Looted <6255880+Looted@users.noreply.github.com>

…ew-comments fix(cli): merge working-tree manifest into staged lookup + dedup toPrologString

Copilot

Pull request overview

This PR improves kibi check --staged traceability resolution by incorporating existing symbol IDs/relationships from the working tree manifest (before applying staged-manifest overrides), and removes duplicated Prolog string encoding to keep serialization consistent across the CLI.

Changes:

Pre-populate manifestLookup from the working-tree config.paths.symbols manifest, then apply staged symbols.yaml overrides.
Deduplicate toPrologString by reusing the shared implementation from ../prolog/codec.
Add a Changeset for a kibi-cli patch release describing both fixes.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 2 comments.

File	Description
packages/cli/src/traceability/temp-kb.ts	Removes the local `toPrologString` helper and imports the shared Prolog codec version.
packages/cli/src/commands/check.ts	Enhances staged-check manifest lookup by seeding it from the working tree manifest prior to staged override parsing.
.changeset/fix-manifest-lookup-and-prolog-codec.md	Documents the behavior change and Prolog codec deduplication for release notes.

Copilot · 2026-04-06T11:14:42Z

+      } catch (e) {
+        // Ignore working-tree manifest parsing errors; staged-only fallback still applies
+        const msg = e instanceof Error ? e.message : String(e);
+        console.debug(`[kibi] skipping working-tree manifest ${absSymbolsPath}: ${msg}`);


console.debug here will emit output unconditionally when the working-tree manifest is invalid, even if the user didn’t enable tracing. Elsewhere (e.g. traceability/git-staged.ts) debug logging is gated behind KIBI_TRACE/KIBI_DEBUG; consider gating this message similarly or routing it through the existing trace mechanism to avoid noisy/unstable CLI output.

Suggested change

console.debug(`[kibi] skipping working-tree manifest ${absSymbolsPath}: ${msg}`);

if (process.env.KIBI_TRACE || process.env.KIBI_DEBUG) {

console.debug(`[kibi] skipping working-tree manifest ${absSymbolsPath}: ${msg}`);

}

Copilot · 2026-04-06T11:14:43Z

+  // Pre-populate lookup from working-tree manifests so that code-only changes
+  // (where symbols.yaml is not staged) still resolve to the correct symbol IDs
+  // and relationships already defined on disk.
+  const config = loadConfig(process.cwd());
+  const symbolsRelPath = config.paths.symbols;
+  if (symbolsRelPath) {
+    const absSymbolsPath = path.resolve(process.cwd(), symbolsRelPath);
+    if (existsSync(absSymbolsPath)) {
+      try {
+        const entries = extractFromManifest(absSymbolsPath);


This change is meant to fix the case where code is staged but symbols.yaml is not; however, the existing --staged tests appear to stage symbols.yaml along with the code. Please add a test that commits a valid symbols.yaml, then stages only a code change, and asserts kibi check --staged still resolves the symbol ID/relationships from the working tree manifest (no hash fallback).

Looted · 2026-04-06T11:18:08Z

@copilot apply changes based on the comments in this thread

Copilot · 2026-04-06T11:18:12Z

@Looted I can’t apply these changes because the pull request’s branch is the repository’s default branch, which I’m not allowed to push to directly.

You can ask me to create a new pull request with the requested changes instead and I'll open a separate PR on a new branch.

Looted · 2026-04-06T11:20:58Z

@Looted I can’t apply these changes because the pull request’s branch is the repository’s default branch, which I’m not allowed to push to directly.

You can ask me to create a new pull request with the requested changes instead and I'll open a separate PR on a new branch.

@copilot Please create a new PR with this work.

Copilot · 2026-04-06T11:21:07Z

@Looted I've opened a new pull request, #140, to work on those changes. Once the pull request is ready, I'll request review from you.

…_DEBUG and add test for code-only staged check Agent-Logs-Url: https://github.com/Looted/kibi/sessions/93b43b29-7204-4f56-82c3-399980819276 Co-authored-by: Looted <6255880+Looted@users.noreply.github.com>

fix(cli): gate working-tree manifest debug log and add code-only staged check test

- Use path.resolve instead of path.join in repo-posture.ts and workspace-health.ts so absolute configured doc roots in .kb/config.json are honored and no longer trigger false-positive bootstrap warnings. - Rebuild packages/cli/src/prolog/codec.js so toPrologAtom and toPrologString are available as named exports at runtime, fixing CLI traceability test imports. - Add missing toPrologAtom/toPrologString mock exports in service.test.ts to prevent Bun mock.module leakage breaking other test files in full-suite runs. - Add regression test for healthy absolute custom doc roots and add staged symbol traceability comments to codec.js.

- workspace-health.ts: restore the legacy >2 missing dirs threshold for root_partial workspaces so small gaps (e.g. flags/events) do not trigger bootstrap nags. This fixes the ~/projects/align regression. - opencode-comment-guidance e2e: bootstrap temp projects with .kb/config.json and required doc directories so the packed plugin sees root_active posture and injects comment guidance as expected.

- discovery-shared.test.ts: add mock.restore() in afterEach to prevent the MockPrologProcess mock from leaking into temp-kb.test.ts during full-suite runs. - service.test.ts: add mock.restore() in beforeEach to prevent the prolog/codec mock from leaking into other tests. This fixes the suite-order-dependent Prolog query failure in temp-kb (projectStagedEntities retract timeout) that only occurred in bun test v1.3.6 (d530ed99) ✓ Created .kb/ directory structure ✓ Created branches/main/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Copied 3 schema files ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents ✓ Created .kb/ directory structure ✓ Created branches/main/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Copied 3 schema files ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents ✓ Created .kb/ directory structure ✓ Created branches/main/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Copied 3 schema files ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents ✓ Created .kb/ directory structure ✓ Created branches/main/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Copied 3 schema files ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents ✓ Created .kb/ directory structure ✓ Created branches/main/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Copied 3 schema files ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents ✓ .kb/ directory already exists, skipping creation ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents ✓ Created .kb/ directory structure ✓ Created branches/main/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Copied 3 schema files ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents ✓ Created .kb/ directory structure ✓ Created branches/main/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Copied 3 schema files ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents ✓ .kb/ directory already exists, skipping creation ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents 📦 Packing packages... Packing packages/core... → kibi-core-0.4.0.tgz Packing packages/cli... → kibi-cli-0.5.0.tgz Packing packages/mcp... → kibi-mcp-0.6.0.tgz 📥 Bootstrapping shared packed test installation... ✓ Created .kb/ directory structure ✓ Created branches/my-branch/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Added .kb/ to .gitignore ✓ Copied 1 schema files ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) ✓ Created .kb/ directory structure ✓ Created branches/main/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Copied 3 schema files ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents ✓ Created .kb/ directory structure ✓ Created branches/main/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Copied 3 schema files ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents ✓ Created .kb/ directory structure ✓ Created branches/main/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Copied 3 schema files ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents ✓ Created .kb/ directory structure ✓ Created branches/main/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Copied 3 schema files ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents ✓ Created .kb/ directory structure ✓ Created branches/main/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Copied 3 schema files ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents ✓ Created .kb/ directory structure ✓ Created branches/main/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Copied 3 schema files Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents ✓ Created .kb/ directory structure ✓ Created branches/main/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Copied 3 schema files ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents but not in isolation.

The script and Docker entrypoint were running bun test v1.3.6 (d530ed99) ✓ Created .kb/ directory structure ✓ Created branches/main/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Copied 3 schema files ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents ✓ Created .kb/ directory structure ✓ Created branches/main/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Copied 3 schema files ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents ✓ Created .kb/ directory structure ✓ Created branches/main/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Copied 3 schema files ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents ✓ Created .kb/ directory structure ✓ Created branches/main/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Copied 3 schema files ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents ✓ Created .kb/ directory structure ✓ Created branches/main/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Copied 3 schema files ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents ✓ .kb/ directory already exists, skipping creation ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents ✓ Created .kb/ directory structure ✓ Created branches/main/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Copied 3 schema files ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents ✓ Created .kb/ directory structure ✓ Created branches/main/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Copied 3 schema files ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents ✓ .kb/ directory already exists, skipping creation ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents 📦 Packing packages... Packing packages/core... → kibi-core-0.4.0.tgz Packing packages/cli... → kibi-cli-0.5.0.tgz Packing packages/mcp... → kibi-mcp-0.6.0.tgz 📥 Bootstrapping shared packed test installation... ✓ Created .kb/ directory structure ✓ Created branches/my-branch/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Added .kb/ to .gitignore ✓ Copied 1 schema files ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) ✓ Created .kb/ directory structure ✓ Created branches/main/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Copied 3 schema files ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents ✓ Created .kb/ directory structure ✓ Created branches/main/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Copied 3 schema files ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents ✓ Created .kb/ directory structure ✓ Created branches/main/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Copied 3 schema files ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents ✓ Created .kb/ directory structure ✓ Created branches/main/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Copied 3 schema files ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents ✓ Created .kb/ directory structure ✓ Created branches/main/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Copied 3 schema files ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents ✓ Created .kb/ directory structure ✓ Created branches/main/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Copied 3 schema files Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents ✓ Created .kb/ directory structure ✓ Created branches/main/ directory ✓ Created config.json with default paths ✓ Added .kb/ to .gitignore ✓ Copied 3 schema files ✓ Installed git hooks (pre-commit, post-checkout, post-merge, post-rewrite) Kibi initialized successfully! Next steps: 1. Run 'kibi doctor' to verify setup 2. Run 'kibi sync' to extract entities from documents without , so they used Bun's default 5000ms per-test timeout. Under full-suite load, integration tests that spawn swipl processes (e.g. ) can exceed 5 seconds and fail intermittently. The script already used ; snip this change makes and the Docker test runner consistent with that configuration, fixing the last intermittent timeout failure.

Looted · 2026-04-07T16:46:38Z

@copilot apply changes based on the comments in this thread in a new pr

Copilot · 2026-04-07T16:46:46Z

@Looted I've opened a new pull request, #141, to work on those changes. Once the pull request is ready, I'll request review from you.

Copilot AI and others added 3 commits April 6, 2026 11:06

fix(cli): add debug trace for working-tree manifest parse failures

6016a23

Agent-Logs-Url: https://github.com/Looted/kibi/sessions/d11497ec-c000-4b40-978d-2f5d5eb012e4 Co-authored-by: Looted <6255880+Looted@users.noreply.github.com>

Merge pull request #138 from Looted/copilot/restore-changes-from-revi…

1268113

…ew-comments fix(cli): merge working-tree manifest into staged lookup + dedup toPrologString

Copilot AI review requested due to automatic review settings April 6, 2026 11:10

Copilot started reviewing on behalf of Looted April 6, 2026 11:11 View session

fix(mcp): accept sourceFile on symbol upserts

7111197

Copilot AI reviewed Apr 6, 2026

View reviewed changes

Initial plan

77aac39

Copilot AI mentioned this pull request Apr 6, 2026

fix(cli): gate working-tree manifest debug log and add code-only staged check test #140

Merged

Copilot AI and others added 9 commits April 6, 2026 11:24

fix(cli): gate working-tree manifest debug log behind KIBI_TRACE/KIBI…

369c732

…_DEBUG and add test for code-only staged check Agent-Logs-Url: https://github.com/Looted/kibi/sessions/93b43b29-7204-4f56-82c3-399980819276 Co-authored-by: Looted <6255880+Looted@users.noreply.github.com>

Merge pull request #140 from Looted/copilot/sub-pr-139

673bfc4

fix(cli): gate working-tree manifest debug log and add code-only staged check test

Merge branch 'develop' of https://github.com/Looted/kibi into develop

7c2ff19

fix(cli): eliminate false startup wait in PrologProcess under Bun

2994632

Revert timeout band-aid in test:unit and Docker entrypoint

b9e189f

Copilot AI mentioned this pull request Apr 7, 2026

Gate working-tree manifest debug log and add code-only staged check test #141

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Merge working-tree manifests with staged overrides and deduplicate Prolog codec#139

Merge working-tree manifests with staged overrides and deduplicate Prolog codec#139
Looted merged 14 commits intomasterfrom
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