Trace code or test a recurring pattern to answer one cited question. Use when: uncertainty needs evidence. Not for external feature teardowns; use reverse-engineer.

Research Answer the caller's bounded question with cited evidence. Choose ordinary investigation, repository tracing or pattern evidence according to the question; these are optional modes, not a sequence. A quick answer needs no report file. Investigation 1. State the question and the decision it informs. Reuse the accepted scope and identify what evidence would answer it; do not expand the objective mid search. 2. Inspect the smallest relevant sources. For changing external facts, use current primary sources. Verify search hits against the actual source. 3. Distinguish observation, inference, contradiction and unknown. Every material claim cites evidence; source agreement does not erase shared provenance. 4. Lead with the answer, then show evidence and remaining gaps. Each part of the question is answered or explicitly unknown with the searched scope disclosed. Code claims cite the observed commit plus file:line . For uncommitted content, state HEAD and the changed file status; do not claim the working bytes can be replayed from HEAD. Keep source identity and freshness visible. Search output, CASS, MS and prior reports are leads, not authority or required phases. Use the current agent by default; additional readers and runtimes require caller selection or existing authorization. For several supplied reports, retain each source's identifier, author/runtime when known and revision/date. Compare claims as agreement, contradiction or unknown while preserving their original evidence. Repeated quotations of one upstream source are not independent corroboration. Verify decisive claims at their source and return one synthesis; do not launch recursive synthesis passes. Repository tracing For a repository model or audit, start from its declared entry points in docs, build manifests or command help and verify them against executable paths. Follow a relevant flow through entry, domain logic, integration and tests; prefer a completed trace to a shallow directory inventory. Report an interrupted trace at its exact file/line and explain what is missing. Choose a useful lens such as persistence, authorization, CLI, build or test without requiring a sweep of every lens. An inline investigation may use dirty working tree evidence with explicit limits. When a durable codebase recon.v1 pack is selected, its stricter contract applies: Write codebase recon.json and a cited codebase recon.md companion at the caller's chosen location, default .agents/scratch/codebase recon/<run id / . Keep mental model, bounded audit, pattern evidence and synthesis distinct. Bind the exact current full commit OID, at least one complete baseline flow, claims with kind, confidence and evidence, and inspected/uninspected scope. Fact and inference citations resolve to repository relative regular files at that commit; the companion report includes line references. Unknowns remain explicit. The manifest report names the companion and its lowercase SHA 256. The companion has one <! codebase recon report.v1 marker and manifest commit , manifest mode , flows sha256 , claims sha256 , and coverage sha256 markers; section digests hash the jq cS output for each section, including its trailing newline. Discover validated priors with skills/research/scripts/codebase recon/validate output.sh repo root <target discover priors . Prefer a verified delta when it answers the request. Delta evidence needs a valid ancestor chain, baseline verified: true and the exact changed paths between the prior and current commits; do not relabel a directory scan as delta. Run skills/research/scripts/codebase recon/validate output.sh repo root <target <recon.json before handoff. It checks both artifacts and rechecks their identities, HEAD and source state; dirty source outside .agents/ cannot satisfy this commit bound pack. Return a validation failure without disguising it as a completed recon pack. Preserve earlier .agents/recon/<run id / packs and their exact cited identities. Prior discovery checks both legacy and current roots; never move or delete old proof to match a new layout. See the [recon scenarios](references/codebase recon/codebase recon.feature). Pattern evidence For a recurring implementation shape, test whether the similarity represents a reusable rule. Record replayable searches, examined hits and exclusions. Align independent implementations by their role in the behavior, then separate required invariants, legitimate variation and incidental syntax. Copies of one lineage do not count as independent evidence. A pattern mining.v1 promotion needs at least three distinct anchored exemplars, a candidate formed before inspecting a separate holdout, a passing holdout and successful back application of every refinement to the original exemplars. Every invariant needs supporting alignment. Otherwise preserve the result as outcome: hypothesis with route: no action ; do not package weak evidence as a rule. For this selected durable mode, write pattern mining.json to .agents/scratch/pattern mining/<run id / or an authorized caller location and run skills/research/scripts/pattern mining/validate output.sh <pattern.json . Preserve the schema's outcome , exemplars , invariants , variations , incidental , holdout , back application and route fields. The compatibility route value operationalize on a valid promotion refers to [Skill Builder's distillation mode](../skill builder/SKILL.md distill expertise); it is not a retired skill invocation or automatic dispatch. Recommend the least committed useful shape: no action, a reference/checklist line, a template, helper or gate. A gate needs demonstrated cost of violation, not merely recurrence. Research returns evidence; adoption remains an explicit caller decision. See [pattern scenarios](references/pattern mining/pattern mining.feature). Output and boundaries Return a cited answer directly unless a durable output was requested or the selected evidence contract requires one. Ordinary durable reports follow [findings.json](schemas/findings.json): question, scope, answer, evidence, contradictions, unknowns, checked and unchecked areas. Multi report synthesis also retains source ledger and comparison . Selected recon and pattern modes retain their own validated formats instead of forcing them into this schema. Use only authorized sources and destinations. For restricted or mined episode material, follow [Memory's access and storage boundary](../memory/SKILL.md). Research selects no work, owns no merged context store, mutates no lifecycle state and issues no semantic verdict. The native caller owns implementation, judgment and completion of the authorized outcome.