feat(git): warn about co-change partners missing from diff and PR

[devin-ai-integration]

Summary

• tracedecay_diff_context and tracedecay_pr_context now return missing_co_change_partners: files that Git history says usually change with a changed file but are not in the change set. For example, a schema change with no matching migration.

Fixes #3015

Motivation

#3015: agents miss companion edits (migrations, fixtures, generated files) that history says go together.

Changes

• New crates/tracedecay-runtime-core/src/git/co_change.rs. It mines up to 1,000 non-merge commits with --no-renames and skips bulk commits that touch more than 50 files. A partner is reported only if it still exists in the target tree. Results are ranked deterministically and capped at 20.
  • Change sets with several files: at least 3 co-changes and coupling of at least 50% of the changed file's commits.
  • Single-file change sets use a stricter gate: at least 5 co-changes and at least 75% coupling.
  • A project that is not a Git repository returns an empty list instead of an error.
• Contracts: new CoChangePartnerV1 { file, partner_of, co_changes, partner_of_changes }. DiffContextResultV1 and all three PrContext*V1 variants (complete, symbols-unavailable, graph-pending) gain a required missing_co_change_partners field.
• Handlers (handlers/git/context.rs):
  • diff context mines HEAD.
  • PR context mines history up to the merge base and checks that partners exist at head.
• Regenerated sdks/typescript/src/operations.ts and updated the SDK decode fixtures.

Test plan

• Behavior test mcp_handler_test::graph_analysis_test::git_context_warns_about_co_change_partners_missing_from_the_change. The fixture repo always changes the schema and its migration together; the feature branch changes the schema without the migration. The test checks the exact partner reported by pr_context and diff_context, and checks that diff_context reports nothing once the migration is in the change set. Before this change the field does not exist, so the test fails.
• Runtime-core unit tests git::co_change::tests::{a_change_missing_its_usual_companion_is_reported,bulk_commits_do_not_couple_files} (run via scripts/require-exact-test.sh … -- --exact)
• mcp_suite tests filtered on context (39 passed) and tracedecay-mcp tests filtered on context (49 passed)
• cargo clippy -p tracedecay-runtime-core -p tracedecay-contracts -p tracedecay-mcp -p tracedecay --features tracedecay/test-transport --all-targets -- -D warnings
• cargo fmt --all -- --check, pnpm --dir dashboard run contracts:check, SDK vitest (37 passed), python3 scripts/linux-test-partitions.py check
• Full cargo nextest run --workspace was not run locally; CI will run it

Checklist

• CHANGELOG.md updated (not done: release-please manages it)
• No secrets, credentials, or .env files included
• Breaking changes documented (if any): the new response field is additive

Link to Devin session: https://app.devin.ai/sessions/12af47e87dd44db6a9c72fdc845270da
Open in Devin Desktop: https://app.devin.ai/desktop/session/12af47e87dd44db6a9c72fdc845270da?variant=devin
Requested by: @ScriptedAlchemy

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[devin-ai-integration]

I'll fix CI failures and address comments from users with write access. I'll skip comments containing "(aside)".

• Disable automatic comment, CI, and merge conflict monitoring

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