fix(index): a full index ends with complete planner statistics (#2571)

[danusha2345]

Fixes #2571.

What happens

After a full codegraph index, the maintenance step runs PRAGMA optimize under PRAGMA analysis_limit=1000. The statistics that leaves are a sample of the first rows of each index. On a repository with one generated file of thousands of symbols — the reporter's Android R.java with 7,728 nodes, a bundled .d.ts with 3,573 — that sample misses the big file, and the planner takes every file for a few symbols: idx_nodes_file_path comes out as 280356 6 where a full ANALYZE gives 280356 32.

With the underestimate, SQLite plans the dominant-file aggregation behind every codegraph_explore as "for every node, scan all nodes in the same file, then probe edges by (source, target)" — quadratic in the big files. The reporter measured ~100 s per explore on a 280k-node index, 1.5 s with exact statistics. The per-process memo from #2086 does not help a CLI explore or the prompt hook, which start a process per call, and in MCP mode the first explore holds the queue for the rest.

The change

A full index now ends with a full ANALYZE (analysis_limit=0) instead of the sampled optimize. It runs where the maintenance already ran — off-thread, after the WAL valve is quiesced — and the reporter's 1 GB index analyzes in 0.77 s, once, at the end of a run that took minutes. A sync keeps the incremental optimize: it re-analyzes only a table that grew by a lot, so the exact statistics a full index leaves stay in place.

runMaintenance takes { fullAnalyze }; indexAll passes it, sync does not.

Test

__tests__/index-full-analyze-stats.test.ts builds a database of one file with 3,000 symbols beside 3,000 files of one, where the big file sorts after the small ones, and reads sqlite_stat1 for idx_nodes_file_path:

• after the sync maintenance: 6000 1 — the sample never reaches the big file;
• after the full-index maintenance: 6000 2 — the exact average.

The second assertion fails on main (runMaintenance takes no options, and the stat stays 6000 1).

🤖 Generated with Claude Code