feat(coding-agents): apply retain attribution to all ingestion paths

[voarsh2]

Extends the coding-agents integration's existing retainTags and retainMetadata support to every document it writes, rather than only live session write-back.

This includes:

• Imported conversations
• Aggregated Git history and full commit documents
• Codebase survey lifecycle documents
• Initiative markers
• Documents saved through hindsight_ingest_document

Configured attribution is merged with each document's built-in tags and metadata, with built-in source identity remaining authoritative.

Why

In shared-bank deployments, consistent attribution is needed to identify and filter documents by project or other configured provenance. Partial attribution leaves Git, survey, and manually ingested documents indistinguishable across projects.

Notes

This is additive and disabled by default. Existing configurations without retainTags or retainMetadata retain their current behavior.

Verification

• 441 coding-agents tests passed
• TypeScript and package build passed
• Declaration generation passed
• Documentation sync passed

[nicoloboschi]

Reviewed and tested locally — rebased onto current main (it was 13 commits behind, predating the cursor fix, Prime Agent and the retainEveryTurns removal) and pushed one cleanup. 462 tests pass, tsc, lint and docs-sync clean.

What's right

The merge order is correct in every path — configured first, built-ins last, deduped:

[...new Set([...(stamp?.tags ?? []), "source:git"])]
{ ...stamp?.metadata, source: "git", repo: repoName, … }

So source identity stays authoritative, and because every path builds its stamp through buildRetainStamp, the reserved-namespace filter comes along for free — a user can't tag a git document harness:codex. Making sessionId optional and resolving it to "unknown" is the right call for documents that have no session.

runtime.toolSpecs() passing repoDir: this.projectDir also quietly fixes a real inconsistency: hindsight_diagnose was reporting process.cwd() rather than the resolved workspace.

What I changed

Both survey-baseline writes branched into two complete client.retain(...) calls differing only in whether { metadata } was passed — six duplicated argument lists, which is where a later edit updates one and misses the other. retain only assigns metadata when truthy, so { metadata: undefined } already omits it and one call covers both cases; that's what knowledge-tools.ts does with Object.keys(metadata).length ? { metadata } : {}. The marker assertion in session-start.test.ts gains the opts argument to match.

I assume the branching existed to keep that assertion passing unchanged — reasonable, but the test was the thing to update.

One thing worth knowing

With retainTags: ["session:{sessionId}"], git and survey documents now carry session:unknown. Documented and honest, but it is new user-visible output; if you'd rather an unresolvable placeholder dropped the tag instead, say so and I'll follow up separately.

Merging once CI is green. Thanks — partial attribution really was the gap, and this closes it cleanly.