feat: dashboard Input/Output Format controls#133
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* docs: add confidence scoring explanation page * docs: fix confidence scoring doc accuracy and default threshold value --------- Co-authored-by: ahfoysal <ahfoysal30@gmail.com>
…kens served) (#123) * docs: token-savings program design spec * fix: resolve 2026-07-03 full-project review findings Config writers (data loss): - string-aware JSONC comment stripping; URLs in values no longer corrupt configs - parse failures skip the file with a warning instead of overwriting user MCP configs - non-dict server sections handled; uninstall matches CCE markers only, never bare "cce" - uninstall strips only the CCE block from shared git hooks Memory (index desync): - bootstrap without sqlite-vec no longer stamps CURRENT_VERSION; vec tables created on later connect - turn re-compression uses DELETE+INSERT so FTS/vec delete triggers fire - compression queue dead-letters after 5 attempts; savings recorded only on success - rollup enqueue dedup via -1 sentinel; PII scrub applied to prompt/tool-payload writes - non-numeric started_at no longer 500s Retrieval/storage (ranking + consistency): - FTS-only chunks get worst-case vector distance instead of perfect 0.0 - FTS queries tokenized per-term (OR-joined, stopwords dropped) instead of one phrase - chunks_vec created with distance_metric=cosine; legacy L2 tables detected and rebuilt - vector/FTS/graph stores roll back on mid-batch failure; FTS re-ingest no longer duplicates Indexer (correctness + secrets): - tree-sitter byte offsets slice bytes, not str; non-ASCII files chunk correctly - single-file target path (watcher) now honors is_secret_file and .cceignore - project_dir resolved once; symlinked roots no longer crash targeted reindex - deleted-but-tracked targets prune index + manifest - unquoted credential assignments redacted; *.env suffix files skipped - Stripe/GitHub vendor regexes fixed (capturing groups leaked full key values) Dashboard (XSS): - all API-sourced strings escaped (sessions, decisions, file paths, chart labels) - inline onclick handlers replaced with data attributes + listeners - state.json written atomically 1040 tests pass (~60 new regression tests, all confirmed failing pre-fix). * docs: Phase 1 retrieval-precision implementation plan * feat(retrieval): persist chunk modified_ts through vector store * feat(indexer): stamp chunks with source file mtime for recency scoring * fix(indexer): stamp git commit chunks with commit-time modified_ts * feat(retrieval): collapse overlapping same-file chunks before packing * feat(retrieval): marginal-utility stop with top-1 guarantee, config-driven * docs: correct omitted-results note design in Phase 1 plan (truthful dropped-count signal) * fix(retrieval): truthful dropped-results signal for the omitted-results note * feat(benchmarks): A/B mode for retrieval precision; tune Phase 1 defaults from evidence Adds --ab flag to run_benchmark.py: indexes the repo once, then runs each query twice (baseline retrieve() vs tuned with threshold+marginal_ratio) and reports per-query token deltas plus aggregate reduction%. Evidence from 6 A/B runs on this repo shows marginal_ratio=0.75 achieves 26.1% token-served reduction with hit rate unchanged (4/8→4/8), clearing the ≥25% gate. confidence_threshold had no effect (all scores 0.70–0.95). Updates retrieval_marginal_ratio default: 0.5 → 0.75. Results committed as benchmarks/results/cce-phase1-ab.{json,md}. * docs(benchmarks): disclose cliff shape and sample-size limits in Phase 1 A/B evidence * fix: point omitted-results note at marginal_ratio; document new retrieval config * fix(indexer): repopulate index after cosine-metric migration The cosine rebuild in VectorStore._ensure_tables wipes on-disk chunks but left manifest.json claiming every file was still indexed, so an incremental reindex (the default for cce index and the watcher) skipped every unchanged file and left context_search returning nothing until cce index --full. VectorStore now flags metric_rebuilt; run_indexing clears the manifest when set, forcing the scan to re-ingest. Mirrors the existing dim-migration guard. Regression test confirms an incremental reindex repopulates post-migration.
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Dashboard format controls from #118 with fixes applied.
What's added
GET /api/formatandPOST /api/formatendpoints persistingtop_k,max_tokens, andoutput_levelinstate.jsoncontext_searchcall — changes apply without a restart; explicit tool arguments still take precedenceFixes applied over #118
POST /api/formatnow usesatomic_write_text(non-atomicwrite_textintroduced the same race conditionset_compressionwas fixed for in fix: full-project review findings + retrieval precision (26% fewer tokens served) #123)_make_servertest helper intest_mcp_server.pynow sets_state_path,_default_top_k, and_default_max_tokens— required by the new_handle_context_searchcode path; absence caused CI failureshasattr(self, "_state_path")guard in_apply_output_compression— the attribute is always initialised in__init__and now always present in test helpersCloses #118