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Andrew Hundt
0370d52f4d
Make index writes and artifact refreshes use verified temp files plus atomic replacement, preserving Windows replace semantics and avoiding fixed temp-path collisions. Thread the remaining pipeline confidence knobs through config while keeping zero-valued defaults backward compatible with existing upstream behavior. Tighten route-node gates and architecture route output so infra URL nodes stay queryable in the graph but do not pollute get_architecture route summaries; preserve code-created absolute URL routes for all language extractors. Harden MCP and CLI path handling around cache paths, grep scratch files, update downloads, checksum validation, stale checks, and project DB discovery without writing protocol noise to stdout. Add regression coverage for corrupt-DB recovery, concurrent atomic writes, tmp-prefixed project DBs, duplicate search result fields, route output filtering, config registry entries, and focused suite selectors. Validated with: git diff --check; make -f Makefile.cbm build/c/test-runner; focused suites security, artifact, graph_buffer, sqlite_writer, store_search, store_bulk, store_pragmas, store_checkpoint, watcher, infrascan, pipeline, store_nodes, mcp, cli, parallel, tool_consolidation, incremental, and store_arch; make -f Makefile.cbm cbm; isolated dogfood index/query run. Signed-off-by: Andrew Hundt <ATHundt@gmail.com>