Align Documentation

Align Documentation

Sync documentation with code after implementation changes. Keep AGENTS.md, API docs, and architecture docs accurate by mapping code changes to their documentation impact.

When to Use

• After completing a feature implementation (post-merge or post-commit)
• After fixing a bug that changes observable behavior
• After a refactoring that renames, moves, or restructures code
• When detect-doc-drift reports findings that need fixing
• When on_post_feature or on_post_merge triggers fire
• NOT during active development — wait until the code is stable
• NOT for creating documentation for a brand-new project (use validate-context-engineering for initial setup)
• NOT for fixing code — this skill only changes documentation

Process

Phase 1: Detect — Identify What Changed

1. Run git diff against the appropriate baseline. Choose the baseline based on context:

   • After a feature: diff against the branch point (git diff main...HEAD)
   • After a bug fix: diff against the commit before the fix
   • After a refactoring: diff against the commit before refactoring started
   • Periodic sync: diff against the last documentation sync commit

2. Extract the list of changed files. For each changed file, note:

   • File path (current and previous if renamed/moved)
   • Nature of change (added, modified, deleted, renamed)
   • Changed exports (new, removed, renamed, signature changed)
   • Changed behavior (different return values, new error types, new side effects)

3. Run harness check-docs to identify any documentation that already has broken references due to the changes.

Graph-Enhanced Context (when available)

When a knowledge graph exists at .harness/graph/, use graph queries for faster, more accurate context:

• query_graph — find documents edges pointing to nodes changed in this diff
• get_impact — auto-suggest which docs need updating after code changes

Replaces manual doc-to-code correlation. Fall back to file-based commands if no graph is available.

Pipeline Context (when orchestrated)

When invoked by harness-docs-pipeline, check for a pipeline field in .harness/handoff.json:

• If pipeline field exists: read DocPipelineContext from it
  • Read pipeline.driftFindings to know which fixes to apply (pre-classified by safety)
  • If pipeline.fixBatch is set, apply only those specific fixes rather than running full detection
  • Write applied fixes as DocFix[] back to pipeline.fixesApplied
  • This enables the convergence loop to track fix verification status
• If pipeline field does not exist: behave exactly as today (standalone mode)

No changes to the skill's interface or output format — the pipeline field is purely additive.

Phase 2: Map — Connect Code Changes to Documentation

For each changed file, identify all documentation that references it:

AGENTS.md sections:

• Knowledge map entries that reference the file path
• Architecture descriptions that mention the module
• Constraint documentation that references the file's layer or patterns
• Onboarding guides that walk through the file

API documentation:

• JSDoc/TSDoc comments in the changed files themselves
• Generated API doc pages that pull from the changed files
• README examples that demonstrate the changed functions
• Tutorial or guide pages that use the changed code

Architecture documentation:

• Diagrams that include the changed module
• Data flow descriptions that reference the changed functions
• Layer descriptions that list the changed file
• Dependency documentation that references the changed imports

Inline code comments:

• Comments in OTHER files that reference the changed file or function
• TODO comments that reference the changed behavior
• Workaround comments that may no longer apply after the change

Phase 3: Generate — Draft Documentation Updates

For each affected documentation location:

1. Draft the specific text change. Show the old text and the new text. Keep the existing style and tone — documentation updates should be invisible in terms of voice.

2. Preserve context. When updating a section, do not just change the specific reference — read the surrounding paragraph and ensure it still makes sense. A renamed function may require updating the explanatory text around it, not just the function name.

3. Handle deletions carefully. When code is deleted, do not just delete the documentation reference. Consider whether the section should be removed entirely, replaced with information about the replacement, or noted as deprecated.

4. Add new sections when needed. If a new module was added, draft a complete documentation section following the existing AGENTS.md structure and style.

Phase 4: Validate — Verify Documentation Accuracy

1. Run harness check-docs to verify all links and references resolve correctly after the updates.

2. Cross-check each update against the actual code. Read the updated documentation and verify every claim by looking at the code. Documentation that is wrong is worse than documentation that is missing.

3. Verify no orphaned references remain. Search documentation files for any remaining references to old names, old paths, or deleted features.

4. Run harness fix-drift to catch any remaining simple drift issues that manual review missed.

Graph Refresh

If a knowledge graph exists at .harness/graph/, refresh it after code changes to keep graph queries accurate:

harness scan [path]

Skipping this step means subsequent graph queries (impact analysis, dependency health, test advisor) may return stale results.

5. Commit the documentation update. Use a commit message that references the original change: "docs: update AGENTS.md for notification service refactoring" or "docs: sync API docs after auth module rename."

What to Update

AGENTS.md Knowledge Map

• File paths and module names (renamed or moved files)
• Module purpose descriptions (changed responsibilities)
• Constraint descriptions (new or changed rules)
• Relationship descriptions (new or changed dependencies)
• Gotcha sections (resolved gotchas, new gotchas)

Inline Code Comments

• Function/class doc comments in the changed files (JSDoc, TSDoc)
• Comments in other files that reference the changed code
• TODO comments that reference completed or changed work
• Workaround comments for issues that may now be resolved

Documentation Pages (docs/)

• API reference pages that describe changed functions
• Architecture pages that diagram changed modules
• Tutorial and guide pages that demonstrate changed code
• Getting-started guides if entry points changed
• Changelog entries for user-facing changes

Harness Integration

• harness check-docs — Run before and after updates. Identifies broken references and validates that all documentation links resolve.
• harness fix-drift — Auto-fix simple drift issues (broken file paths, renamed references) after manual review confirms correctness.
• harness fix-drift --json — Machine-readable output for tracking what was auto-fixed.
• harness validate — Run after documentation changes to verify overall project health is maintained.

Success Criteria

• harness check-docs passes with zero errors after documentation updates
• Every code change from the diff has been mapped to its documentation impact
• All file paths in documentation match current file locations
• All function/class names in documentation match current code
• All behavioral descriptions in documentation match current implementation
• Documentation updates are committed with clear references to the triggering code change
• No orphaned references to old names, paths, or deleted features remain

Rationalizations to Reject

Examples

Example: Syncing docs after a module rename

Code change: src/services/mailer.ts renamed to src/services/email-service.ts. Functions sendMail() and formatMailBody() renamed to sendEmail() and formatEmailBody().

Documentation impact map:

AGENTS.md:34      — "mailer.ts handles email delivery" → update path and description
AGENTS.md:78      — "Use sendMail() for all outbound email" → update function name
docs/api.md:156   — sendMail() API reference → update name and import path
docs/arch.md:45   — architecture diagram lists "mailer" → update to "email-service"
src/controllers/user-controller.ts:12 — comment "// delegates to mailer" → update

Updates applied:

• AGENTS.md: updated two sections with new file path and function names
• docs/api.md: updated function reference and import example
• docs/arch.md: updated module name in architecture description
• src/controllers/user-controller.ts: updated inline comment

Validation: harness check-docs passes. All references resolve. Commit: "docs: sync documentation after mailer rename to email-service"

Example: Syncing docs after adding error handling

Code change: createUser() in src/services/user-service.ts now throws ValidationError instead of returning null on invalid input.

Documentation impact map:

docs/api.md:89    — "Returns null if validation fails" → update to describe thrown error
AGENTS.md:52      — No mention of error handling → add note about ValidationError
src/services/user-service.ts:15 — JSDoc @returns tag → update, add @throws tag

Updates applied:

• docs/api.md: replaced "returns null" with "throws ValidationError" and added example
• AGENTS.md: added note about error handling pattern in user-service section
• JSDoc: updated @returns, added @throws ValidationError

Validation: harness check-docs passes. Commit: "docs: update documentation for createUser error handling change"

Escalation

• When you cannot determine what documentation is affected: Run harness check-docs for automated detection. For manual analysis, search all .md files and code comments for the old name/path. If the change is large, use detect-doc-drift first to get a complete inventory.
• When documentation is in an external system (wiki, Confluence): Document the needed change and flag it for manual update. Include the specific text that needs changing and the correct replacement.
• When the code change is so large that documentation needs a rewrite: Break the documentation update into sections. Update one section at a time, validating after each. Do not attempt a full rewrite in one pass.
• When you disagree with the existing documentation style: Follow the existing style. Documentation alignment is about accuracy, not style improvement. Style changes should be a separate, deliberate effort.