fix(index): key files by project, exact-match callers, auto-prune, honor skip patterns

[ajianaz]

What

Four index data-correctness fixes: files keyed by (project_id, path) (schema v8), exact-match call graph lookups, automatic pruning of stale files on every index run, and skip patterns honored by every index entry point.

Why

• files.path was a global PRIMARY KEY with ON CONFLICT(path), so two projects with the same relative path overwrote each other's fingerprint/project_id and reindexed forever.
• find_callers/find_callees/trace_path used LIKE '%name%': removing run flagged callers of rerun, and _/% acted as wildcards. This feeds index-breaking-change (Major), impact_analysis and trace_path.
• prune_deleted only ran under --prune and did not touch edges.
• cora serve and cora index --watch called index_project (no skip patterns), undoing ignore.files / index.skip_files.

How

• Migration v8 rebuilds files in one transaction with PRIMARY KEY (project_id, path); rows with NULL project_id (pre-v2 orphans) are dropped and recreated on next index. Upsert uses ON CONFLICT(project_id, path).
• Call graph/edge queries use = ?1. Callees are already normalized to bare names at extraction, so exact match is correct; impact_analysis recursion is covered by a test.
• index_project_with_id records the walked file set and prunes stored files not in it (deleted, gitignored, newly excluded) via a shared prune_paths that clears symbols, call_graph, edges and files. prune_deleted (--prune) uses the same helper.
• New index::prepare_index_config / skip_patterns_from_config used by index, --watch and serve. index_project is now test-only so production cannot regress to no-skip.

Testing

• cargo test --features tree-sitter passes
• cargo fmt --all -- --check passes
• cargo clippy --all-targets --features tree-sitter -- -D warnings passes
• cargo build --release --features tree-sitter passes (not run locally)
• Manual smoke-test (covered by tests only)

New tests: v7 -> v8 migration (data kept, orphan dropped, idempotent, two projects share a path); two real projects with same path both go up to date; run vs rerun/get_users wildcard and %; impact_analysis/trace_path recursion; auto-prune clears symbols/call_graph/edges/files; --prune clears edges; skip pattern resolver + exclusion.

Not in this PR: unused-imports, per-language call nodes, vector lock.

Related Issues

None.

Checklist

• Branch name follows convention (fix/)
• Branch is from develop
• Commit messages follow Conventional Commits
• No secrets or credentials committed
• One logical change per PR (index data correctness)

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