Agent Skills: Knowledge Synthesis

Codex compatibility note:

• Invoke repository skills with $skill-name in Codex; this mirrored copy rewrites legacy Claude /skill-name references.
• Task tracker mandate: BEFORE executing any workflow or skill step, create/update task tracking for all steps and keep it synchronized as progress changes.
• User-question prompts mean to ask the user directly in Codex.
• Ignore Claude-specific mode-switch instructions when they appear.
• Strict execution contract: when a user explicitly invokes a skill, execute that skill protocol as written.
• Subagent authorization: when a skill is user-invoked or AI-detected and its protocol requires subagents, that skill activation authorizes use of the required spawn_agent subagent(s) for that task.
• Do not skip, reorder, or merge protocol steps unless the user explicitly approves the deviation first.
• For workflow skills, execute each listed child-skill step explicitly and report step-by-step evidence.
• If a required step/tool cannot run in this environment, stop and ask the user before adapting.

Codex Project-Reference Loading (No Hooks)

Codex uses static project-reference loading instead of runtime-injected project docs. When coding, planning, debugging, testing, or reviewing, open project docs explicitly using this routing.

Always read:

• docs/project-config.json (project-specific paths, commands, modules, and workflow/test settings)
• docs/project-reference/docs-index-reference.md (routes to the full docs/project-reference/* catalog)
• docs/project-reference/lessons.md (always-on guardrails and anti-patterns)

Missing/stale context route: If docs/project-config.json, the docs index, lessons.md, CLAUDE.md, AGENTS.md, or any task-required reference doc is missing or stale, auto-run $project-init or the narrow setup route ($project-config, $docs-init, $scan-all, $scan --target=<key>, $claude-md-init) before ordinary project-specific work. If Codex mirrors or AGENTS.md are missing/stale, ask the user to run $sync-codex; do not auto-run it.

Situation-based docs:

• Backend/CQRS/API/domain/entity changes: backend-patterns-reference.md, domain-entities-reference.md, project-structure-reference.md
• Frontend/UI/styling/design-system: frontend-patterns-reference.md, scss-styling-guide.md, design-system/README.md
• Spec authoring, docs/specs/ pathing, or TC format: feature-spec-reference.md, spec-system-reference.md, spec-principles.md
• Behavior/public-contract changes or spec-test-code sync: workflow-spec-test-code-cycle-reference.md plus the spec docs above
• Derived spec indexes/ERDs/reimplementation guides: spec-system-reference.md and source Feature Specs under docs/specs/
• Integration test implementation/review: integration-test-reference.md
• E2E test implementation/review: e2e-test-reference.md
• Code review/audit work: code-review-rules.md plus domain docs above based on changed files

Do not read all docs blindly. Start from docs-index-reference.md, then open only relevant files for the task.

Quick Summary

Goal: Produce a fully-cited, template-compliant research report by synthesizing the evidence base using the enforced template — whose confidence scores and gaps are honest enough to trust for decisions.

Summary:

• Synthesizes a report FROM an existing evidence base (.claude/tmp/_evidence-{slug}.md + _sources-{slug}.md from deep-research) — this skill does not gather sources, it consolidates them into docs/knowledge/research/{slug}.md.
• The enforced template (.claude/templates/research-report-template.md) is non-negotiable: every section MUST appear, and the Knowledge Gaps section can never be omitted — a missing gaps section manufactures false confidence.
• Citation discipline is the core gate: every factual claim carries an inline [N], every Sources-table entry is referenced at least once, and there are zero orphan citations or orphan sources.
• Close with an honest confidence rollup (weighted average of finding scores) that prominently flags any <60% finding, then clean up .claude/tmp/ working files.

Workflow:

1. Load evidence — Read evidence base from deep-research
2. Load template — Read enforced template from .claude/templates/
3. Synthesize — Write report following template structure
4. Citation check — Verify every claim has citation
5. Confidence summary — Aggregate scores, flag gaps

Key Rules:

• MUST ATTENTION use enforced template structure — all sections required
• Every factual claim inline-cited: [N] referencing source table
• Knowledge gaps section mandatory

Be skeptical. Apply critical thinking, sequential thinking. Every claim needs traced proof, confidence percentages (Idea should be more than 80%).

Knowledge Synthesis

Knowledge Work Rules

Web Research Protocol — Every factual claim needs 2+ independent sources. Source tiers: Tier 1 (authoritative .gov/.edu/official docs), Tier 2 (industry reports), Tier 3 (credible blogs — cross-validate), Tier 4 (unverified — NEVER cite as fact). Declare confidence (95/80/60/<60%) for all findings. Use the enforced template structure — all sections required. Working files → .claude/tmp/, final output → docs/knowledge/. Canonical protocol lives in the web-research skill.

Step 1: Load Evidence

Read .claude/tmp/_evidence-{slug}.md and .claude/tmp/_sources-{slug}.md.

Inventory:

• Total findings with confidence scores
• Unresolved discrepancies
• Remaining gaps

Step 2: Load Template

Read enforced template: .claude/templates/research-report-template.md

Every template section MUST ATTENTION appear in final report.

Step 3: Synthesize Report

Write to docs/knowledge/research/{slug}.md. For each template section:

1. Map relevant findings from evidence base
2. Write content with inline citations [N]
3. Declare confidence per finding
4. Note cross-cutting patterns and contradictions in Analysis section

Step 4: Citation Audit

Verify:

• Every factual claim has 1+ [N] citation
• Every source in Sources table referenced 1+ time
• No orphan citations (referencing non-existent source)

Step 5: Confidence Summary

Calculate overall report confidence:

• Average of all finding confidence scores
• Weight by finding importance
• Flag any <60% findings prominently

Output

Final report: docs/knowledge/research/{descriptive-slug}.md

Clean up working files from .claude/tmp/ after successful synthesis.

[IMPORTANT] Use task tracking to break ALL work into small tasks BEFORE starting.

AI Mistake Prevention — Failure modes to avoid on every task:

Re-read files after context changes. Context compaction, resume, or long-running work can make memory stale; verify current files before acting. Verify generated content against source evidence. AI hallucinates APIs, names, claims, and document facts. Check the relevant source before documenting or referencing. Check downstream references before deleting or renaming. Removing an artifact can stale docs, generated mirrors, configs, and callers; map references first. Trace the full impact chain after edits. Changing a definition can miss derived outputs and consumers. Follow the affected chain before declaring done. Verify ALL affected outputs, not just the first. One green check is not all green checks; validate every output surface the change can affect. Assume existing values are intentional — ask WHY before changing. Before changing a constant, limit, flag, wording, or pattern, read nearby context and history. Surface ambiguity before acting — don't pick silently. Multiple valid interpretations require an explicit question or stated assumption with risk. Keep shared guidance role-relevant. Universal guidance must help every receiving skill or agent; code-specific obligations belong only in code-specific protocols.

Critical Thinking Mindset — Apply critical thinking, sequential thinking. Every claim needs traced proof, confidence >80% to act. Anti-hallucination: Never present guess as fact — cite sources for every claim, admit uncertainty freely, self-check output for errors, cross-reference independently, stay skeptical of own confidence — certainty without evidence root of all hallucination.

MUST ATTENTION apply critical + sequential thinking — every claim needs appropriate traced evidence (file:line for repo/code claims; source URL or artifact section for research, product, content, and docs claims); confidence >80% to act, <60% DO NOT recommend. Anti-hallucination: never present guess as fact, admit uncertainty freely, cross-reference independently, stay skeptical of own confidence.

MUST ATTENTION apply AI mistake prevention — verify generated content against evidence, trace downstream references before deleting or renaming, verify all affected outputs, re-read files after context loss, and surface ambiguity before acting.

Closing Reminders

IMPORTANT MUST ATTENTION Goal: Produce a fully-cited, template-compliant research report by synthesizing the existing evidence base through the enforced template — whose confidence scores and Knowledge Gaps are honest enough to trust for decisions.

Protocols in force (concise digest of the SYNC/shared blocks this skill carries): MUST ATTENTION honor every block below — each is a signpost to its canonical body above.

• AI Mistake Prevention: verify generated content against evidence, trace downstream references, verify all affected outputs, re-read after context loss, surface ambiguity.
• Critical Thinking: traced proof per claim, confidence >80% to act, never guess as fact.

IMPORTANT MUST ATTENTION use enforced template structure (.claude/templates/research-report-template.md) — every section required, NEVER omit Knowledge Gaps — why: a missing gaps section manufactures false confidence in incomplete research IMPORTANT MUST ATTENTION inline-cite every factual claim with [N]; verify zero orphan citations (claim cites missing source) AND zero orphan sources (Sources-table row referenced 0 times) — why: uncited claims are assertions, not findings IMPORTANT MUST ATTENTION synthesize FROM the evidence base only (.claude/tmp/_evidence-{slug}.md + _sources-{slug}.md) — NEVER fabricate, add, or upgrade findings beyond gathered evidence; this skill consolidates, it does not research — why: invented findings poison the report's trust IMPORTANT MUST ATTENTION respect source tiers — Tier 4 (unverified) NEVER cited as fact; every factual claim backed by 2+ independent sources — why: single-source or unverified claims read as confident but unproven IMPORTANT MUST ATTENTION close with an honest confidence rollup (importance-weighted average of finding scores) that prominently flags every <60% finding — why: an unflagged weak finding inflates apparent report confidence IMPORTANT MUST ATTENTION break work into small todo tasks using task tracking BEFORE starting; mark one in_progress at a time and complete it on evidence IMPORTANT MUST ATTENTION cite file:line evidence (or [N] source) for every claim — confidence >80% to act, <60% DO NOT assert; NEVER present a guess as fact IMPORTANT MUST ATTENTION grep/read 3+ similar existing reports under docs/knowledge/research/ before writing — match the template's section shape, do NOT invent a new layout — why: divergent report structure breaks the knowledge-review gate IMPORTANT MUST ATTENTION output final report to docs/knowledge/research/{slug}.md, then clean up .claude/tmp/ working files after successful synthesis — why: stale working files leak across runs IMPORTANT MUST ATTENTION add a final review todo task to verify work quality (template complete · citations balanced · gaps present · rollup flagged)

Anti-Rationalization:

| Evasion | Rebuttal | | -------------------------------------------- | ---------------------------------------------------------------------------------- | | "Evidence is thin, fill the gap with my own" | NEVER fabricate. Record it in Knowledge Gaps with confidence <60% instead. | | "This claim is obvious, skip the citation" | No [N] = not a finding. Cite the source or move it to assumptions. | | "Gaps section is empty, drop it" | Empty ≠ omit. State "no unresolved gaps" explicitly — omission fakes completeness. | | "All findings strong, skip the rollup flag" | Compute the weighted average; flag any <60%. One weak finding hides in the mean. | | "Template section is N/A, delete it" | Keep it, write "Not applicable — why". Missing sections fail the knowledge-review. |

IMPORTANT MUST ATTENTION Goal echo: fully-cited, template-compliant report; NEVER omit Knowledge Gaps; zero orphan citations/sources — synthesize FROM evidence, never fabricate.

Hookless Prompt Protocol Mirror (Auto-Synced)

Source: .claude/.ck.json + .claude/skills/shared/sync-inline-versions.md (:full blocks) + .claude/scripts/lib/hookless-prompt-protocol.cjs

[WORKFLOW-EXECUTION-PROTOCOL] [BLOCKING] Workflow Execution Protocol — MANDATORY IMPORTANT MUST CRITICAL. Do not skip for any reason.

Generic portability boundary: Reusable skills and protocol text stay project-neutral; project-specific conventions are discovered from docs/project-config.json and docs/project-reference/. Apply shared AI-SDD from shared/sdd-artifact-contract.md. Read docs/project-config.json and docs/project-reference/docs-index-reference.md, then open the project reference docs named there. For spec, test-case, behavior-change, public-contract, or docs/specs/ work, route through the local spec docs named by the docs index: feature-spec-reference.md, spec-system-reference.md, spec-principles.md, and workflow-spec-test-code-cycle-reference.md when specs/tests/code must stay synchronized. If either file or a required reference doc is missing or stale, auto-run $project-init (or the narrow lower-level route such as $project-config, $docs-init, $scan-all, or $scan --target=<key>) before ordinary project-specific work. Any supported AI tool may execute when this shared context and local docs are available.

1. DETECT: If the prompt starts with an explicit slash skill/workflow command, execute it directly. Otherwise match the prompt against the workflow catalog and skill list.
2. ANALYZE: Choose the best option: execute directly, invoke a skill, activate a standard workflow, or compose a custom step combination.
3. AUTO-SELECT: Pick the best option yourself. Do not ask the user to choose between direct execution, skill, standard workflow, or custom workflow.
4. ACTIVATE: For a selected workflow, call $start-workflow <workflowId>; for a selected skill, invoke that skill; for a custom workflow, sequence custom steps directly; for direct execution, proceed with the task.
5. CREATE TASKS: task tracking for ALL workflow/skill/custom steps before execution when the selected path has multiple steps.
6. EXECUTE: Advance per the Workflow Step Advancement & Parallel Phases rule in your context instructions — model-driven; a sub-agent completion advances a step identically to an inline call; a parallel-phase group is an all-return barrier (advance only after ALL members return, never serialize it)

Shared AI-SDD Protocol Markers

Source: .claude/skills/shared/sync-inline-versions.md

SYNC:ai-sdd-artifact-contract

AI-SDD Artifact Contract — Shared spec-driven development rules stay portable and source-owned.

1. Keep reusable AI-SDD principles in .claude; put repository-specific paths, commands, owners, products, and formats in project config/reference docs.
2. Preserve cycle: spec -> plan -> tasks -> implement -> verify -> update spec/docs.
3. Trace every requirement or invariant through decision, task, TC/test, source evidence, and docs/spec update.
4. Treat code-to-spec extraction as reference-only until accepted by the canonical spec owner.
5. Any supported AI tool may plan, implement, review, or verify with synced context; using multiple tools is optional.
6. Update .claude source first, then sync generated mirrors; do not manually edit .agents, .codex, or AGENTS.md. — why: mirrors are generated artifacts; hand-edits are overwritten on the next sync
7. If docs/project-config.json, root instruction files, or a required project-reference doc is missing or stale, auto-run $project-init or the narrow lower-level route before ordinary project-specific work.

Active reference: shared/sdd-artifact-contract.md in the active skills root.

SYNC:ai-sdd-artifact-contract:reminder

• MANDATORY Apply shared/sdd-artifact-contract.md; keep reusable AI-SDD in .claude and local rules in project docs.
• MANDATORY Code-to-spec extraction is reference-only until canonical acceptance; any supported AI tool may execute with synced context.
• MANDATORY Update .claude source before syncing generated mirrors; do not manually edit .agents, .codex, or AGENTS.md.
• MANDATORY Missing or stale project config, root instruction files, or required reference docs route project-specific work through $project-init or the narrow setup route automatically. [TASK-PLANNING] [MANDATORY] BEFORE executing any workflow or skill step, create/update task tracking for all planned steps, then keep it synchronized as each step starts/completes.

[LESSON-LEARNED-REMINDER] [BLOCKING] Task Planning & Continuous Improvement — MANDATORY. Do not skip.

Break work into small tasks (task tracking) before starting. Add final task: "Analyze AI mistakes & lessons learned".

Extract lessons — ROOT CAUSE ONLY, not symptom fixes:

1. Name the FAILURE MODE (reasoning/assumption failure), not symptom — "assumed API existed without reading source" not "used wrong enum value".
2. Generality test: does this failure mode apply to ≥3 contexts/codebases? If not, abstract one level up.
3. Write as a universal rule — strip project-specific names/paths/classes. Useful on any codebase.
4. Consolidate: multiple mistakes sharing one failure mode → ONE lesson.
5. Recurrence gate: "Would this recur in future session WITHOUT this reminder?" — No → skip $learn.
6. Auto-fix gate: "Could $code-review/$code-simplifier/$security-review/$lint catch this?" — Yes → improve review skill instead.
7. BOTH gates pass → ask user to run $learn. [CRITICAL-THINKING-MINDSET] Apply critical thinking, sequential thinking. Every claim needs traced proof, confidence >80% to act. Anti-hallucination principle: Never present guess as fact — cite sources for every claim, admit uncertainty freely, self-check output for errors, cross-reference independently, stay skeptical of own confidence — certainty without evidence root of all hallucination. AI Attention principle (Primacy-Recency): Put the 3 most critical rules at both top and bottom of long prompts/protocols so instruction adherence survives long context windows. Goal-driven execution: Define success criteria first, loop until verified, and stop only when observable checks pass. Tests verify intent: Tests must protect business rules/invariants and fail when the protected intent breaks, not only mirror current behavior.

Common AI Mistake Prevention (System Lessons)

• Re-read files after context compaction. Edit requires prior Read in same context; compaction wipes read state. Re-read before editing.
• Grep for old terms after bulk replacements. AI over-trusts find/replace completeness. Grep full repo after bulk edits for missed refs in docs/configs/catalogs.
• Check downstream references before deleting. Deletions cascade doc/code staleness. Map referencing files before removal.
• After memory loss, check existing state before creating new. Compaction wipes prior-work memory. Query current state to resume — never blindly duplicate.
• Verify AI-generated content against actual code. AI hallucinates APIs, class names, method signatures. Grep to confirm existence before documenting/referencing.
• Trace full dependency chain after edits. Changing a definition misses downstream consumers. Trace the full chain.
• When renaming, grep ALL consumer file types. Some file types silently ignore missing refs (no compile error). Search code, templates, configs, generated files.
• Trace ALL code paths when verifying correctness. Code existing ≠ code executing. Trace early exits, error branches, conditional skips — not just happy path.
• Update docs that embed canonical data when source changes. Docs inlining derived data (workflows, schemas, configs) go stale silently. Update all embedding docs alongside source.
• Verify sub-agent results after context recovery. Background agents may finish while parent compacted — grep-verify output, don't trust assumed completion.
• Cross-check full target list against sub-agent assignments. Parallel sub-agents by category miss boundary items. Reconcile union of assignments against target list before proceeding.
• Sub-agents inherit knowledge only from their agent .md definition — use custom agent types, not built-in Explore. Tool adoption = permission + knowledge + enforcement (numbered workflow step).
• Persist sub-agent findings incrementally, not as a final batch. Long sub-agents hit cutoffs before final write — findings lost. Instruct append-per-section to report file.
• When debugging, ask "whose responsibility?" before fixing. Trace caller (wrong data) vs callee (wrong handling). Fix at responsible layer — never patch symptom site.
• Grep ALL removed names after extraction/refactoring. Primary file "done" ≠ secondary files clean. Grep entire scope for every removed symbol before declaring complete.
• Assume existing values are intentional — ask WHY before changing. Pattern-matching as "wrong" skips context. Before changing any constant/limit/flag: read comments, git blame, surrounding code.
• Verify ALL affected outputs, not just the first. One build green ≠ all green. Multi-stack changes (backend/frontend/tests/docs) require verifying EVERY output.
• Evaluate fit before copying a nearby pattern. Closest example ≠ matching preconditions — verify the new context shares the same constraints, base classes, scope, lifetime.
• Holistic-first debugging — resist nearest-attention trap. Don't dive into first plausible cause. List EVERY precondition (config, env vars, paths, DB, endpoints, creds, versions, DI, data). Verify each against evidence (grep/query — not reasoning). Ask "what would falsify this?" — if nothing, it's not a hypothesis. Most expensive failure: going deeper in "obvious" layer while bug sits in layer never questioned.
• Surgical changes — apply the diff test (context-aware). Two modes: (1) Bug fix → every line traces to the bug; no restyling; orphan cleanup only for imports YOUR changes made unused. (2) Review/enhancement → implement improvements AND announce as "Enhancement beyond main request: [what]". Never silently scope-creep. Diff test: "Would this line exist if I wasn't asked to do X?" — if no, delete or announce.
• Surface ambiguity before coding — don't pick silently. Multiple valid interpretations → present each with effort: "[Request] could mean (1) [N h], (2) [N h]. Which matters?" List scope/format/volume/constraints assumptions first. If simpler path exists, say so. Never silently pick.
• [MANDATORY FIRST ACTION] ALWAYS activate a suitable skill or workflow BEFORE responding. Match task against workflow catalog + skill list; invoke via skill invocation or $start-workflow <workflowId>. NEVER answer or write code before checking. Skip = protocol violation.
• Why-Review adversarial mindset — apply when reviewing any plan, decision, or design. Default SKEPTIC not VALIDATOR: steel-man a rejected alternative, invert each stated reason ("what does it sacrifice?"), stress-test top 2-3 assumptions, run pre-mortem ("ships, fails in 3 months — what breaks?"), surface 1-2 alternatives author missed. Section presence ≠ quality; quality = causal reasoning + concrete mitigations + evidence, not "it's better" or "monitor closely".
• Front-load report-write in sub-agent prompts for large reviews. Many-file sub-agents hit budget before final write — findings lost. Design prompts so: (1) report-write is first explicit deliverable, (2) append per-file/section (not batched), (3) scope bounded so reads don't exhaust budget. Truncated mid-sentence with no report file → spawn narrower scope, don't retry same prompt.
• After context compaction, re-verify all prior phase outcomes before continuing. Summaries describe intent, not environment state (git index, filesystem, processes). On resume, FIRST audit: git status, re-read modified files, verify filesystem. Every "completed" claim is an untested hypothesis until evidence confirms.
• OOM/memory: check row count before row size. Triage: (1) Unbounded query — no DB filter for trigger? Push filter to DB; eliminates OOM. (2) Large rows? Projection reduces proportionally. Row reduction > projection in ROI.
• Keep domain concepts out of generic/shared/infrastructure layers. Reusable layer (shared library, framework, infra module) must reference NO consumer-specific domain concept — tenant/customer/product IDs, business entities, feature rules. Leak compiles + runs → passes review silently while coupling the "reusable" layer to one consumer. Keep shared type domain-free; push domain fields/logic down into the consumer via subclass/composition. — why: a layer coupled to one consumer's domain is no longer reusable.