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True incremental indexing: clean-rebuild parity, 6x post-edit indexing speedup, explicit freshness, and graph-derived search ranking - #1245

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ahundt wants to merge 1013 commits into

DeusData:mainfrom

ahundt:api-consolidation

Draft

True incremental indexing: clean-rebuild parity, 6x post-edit indexing speedup, explicit freshness, and graph-derived search ranking#1245
ahundt wants to merge 1013 commits into
DeusData:mainfrom
ahundt:api-consolidation

This pull request is big! We're only showing the most recent 250 commits

Commits on Jul 25, 2026
- test(pipeline): preserve graph on unreadable coverage
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- fix(metadata): persist complete dirty-file observations
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- refactor(git): execute repository queries with literal argv
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- test(c-lsp): resolve xxhash fixture from runner image
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- test(py-lsp): measure scale guard with process CPU time
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- fix(platform): reject truncated environment values
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- fix(mcp): use configured auto-index admission helper
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- fix(build): give analyzer the test harness include path
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- fix(build): propagate Clang analyzer failures
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- build(test-syntax): reuse the real C test flags
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- test(mcp): keep environ declaration POSIX-only
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- fix(build): preserve leak command status under /bin/sh
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- refactor(json): share exact escaped-length accounting
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- refactor(config): share query output byte definitions
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Commits on Jul 26, 2026
- fix(cypher): separate output caps from working budgets
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- fix(depindex): rank from every project import
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- fix(depindex): stream every project import edge
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- fix(depindex): stream every dependency module
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  95b7866
- fix(mcp): list every indexed dependency
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  668a7d0
- fix(store): rank every fallback package before preview
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  2f4403b
- fix(cli): state query budget exhaustion as an MCP error
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  8bae19e
- fix(store): select route preview after filtering
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  89fa0b9
- fix(store): classify layers from exact boundaries
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- fix(store): retain every file-tree directory
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  c0fd3fa
- fix(store): omit prefix clusters beyond node budget
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- fix(cypher): bind variables beyond inline storage
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- fix(pipeline): scan complete cross-repo edge streams
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- refactor(config): share search preview defaults
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- fix(pipeline): match complete Kubernetes selector sets
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  f8b413b
- fix(extraction): resolve channel constants past 256 bindings
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  eccd11b
- fix(watcher): persist dirty paths past 4096 entries
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- test(main): select env-filtered suites from canonical registry
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- fix(extraction): report every detected parse-error region
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  046baa4
- fix(semantic): reject incomplete corpus batches
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  11c90a3
- fix(semantic): tokenize complete function metadata
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  bf58de7
- fix(minhash): hash complete function syntax
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- fix(semantic): report bounded candidate omissions
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  d990e8a
- fix(semantic): rank bounded LSH candidates by band evidence
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  43ce3a9
- fix(similarity): report bounded LSH query omissions
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  2d0808f
- fix(fqn): retain path components past inline storage
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  3cb7d92
- fix(githistory): retain all temporal file paths
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  927fcfb
- fix(githistory): rank bounded coupling edges deterministically
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  f340698
- fix(githistory): retain exact coupling paths
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  c10470a
- feat(githistory): configure coupling output budget
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  493e104
- fix(extraction): retain infra bindings past eight entries
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- fix(extraction): retain every Go result type
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  41ec1b6
- fix(cypher): execute literal UNWIND bindings
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  e242aca
- fix(extraction): retain base classes beyond 15
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  b97256d
- fix(extraction): retain scopes beyond 64
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  d5f6ecf
- fix(extraction): retain complexity beyond 4095 branches
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  817708d
- fix(extraction): retain imports after 16 script blocks
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  98297ec
- fix(ast-profile): remove 2048-frame traversal cap
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  e85a91c
- fix(extraction): resolve Nickel calls past 8 wrappers
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  4ec3d34
- test(pipeline): preserve dirty ledger after capped fallback failure
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  e36dcde
- fix(pipeline): cancel index requests waiting on global lock
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  3e011a0
- test(mcp): assert sync autoindex leaves rank views complete
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  2346459
- fix(pipeline): export artifacts after graph publication
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  8d1f3e0
- fix(cli): migrate retired config spellings transactionally
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  d9345ab
- fix(benchmarks): parse tool payload after MCP update notice
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  82269dd
- fix(benchmarks): read worker metrics from daemon log
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Commits on Jul 27, 2026
- fix(semantic): scan escaped JSON metadata to closing delimiters
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  01167d7
- fix(search): aggregate summary facets across every filtered node
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  fbc3208
- fix(mcp): attach project status to the first tool response
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  111d426
- fix(extract,mcp): retain pointer returns and exact signature status
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  c51e5cb
- fix(cli): distinguish activation refusal states
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  b3fd2f3
- fix(extract,mcp): retain cfg predicates and report rank state
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  a28133a
- fix(mcp): retain auto-index recovery in project errors
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  e332a1c
- fix(mcp): expose stale architecture status in TOON
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  bad6493
- fix(mcp): omit stale ranks from architecture resources
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  c3b5b05
- fix(mcp): resolve session store for first inventory context
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  8f679a2
- fix(mcp): let parent own supervised index context
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  e11a127
- fix(mcp): name visible source tool in initialize
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  f24ef08
- fix(rust): exclude macro and ambiguous member CALLS edges
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  e4f8328
- fix(mcp): bind first index context to published project
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  87c8fdd
- fix(mcp): return recovery metadata for missing indexes
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  917ed85
- fix(benchmarks): clean invalidated candidate objects
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- fix(benchmarks): record Makefile compiler identity
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- fix(benchmarks): record self-dogfood comparison manifests
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- fix(cli): stop advertising deprecated inline JSON
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- fix(config): use live daemon settings and shared architecture defaults
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  17eba00
- src/mcp/mcp.c: preserve UTF-8 in search_code output
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- fix(mcp): parse current search_graph JSON in smoke harness
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- fix(smoke): bind fault baselines to worker argv
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  5c94d53
- fix(benchmarks): select CLI transport for active-daemon matrices
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- feat(benchmarks): materialize ref candidates and explicit CBM environments
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  c018539
- feat(benchmarks): isolate exact-build matrices in named Docker volumes
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  ae6e12f
- fix(sqlite_writer): initialize metadata page roots for GCC
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  f688d04
- fix(benchmarks): retain container manifests and failed build logs
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  937bb79
- fix(benchmarks): copy manifests below the results-volume root
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  c72bfb1
- fix(benchmarks): isolate named histories by measurement cohort
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  4b515bb
- feat(benchmarks): record shared C and C++ build settings
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  e3e1bf9
- fix(benchmarks): key Docker resumes by Git refs
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  f1428a9
- feat(benchmarks): search moved candidate worktree roots
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  20ad7e8
- feat(benchmarks): default Docker cohorts to Clang 18
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Commits on Jul 28, 2026
- perf(index): batch Git context and bound descriptor-close work
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  e2ff67f
- pipeline.c, test_pipeline.c: run Git scan concurrently with graph postpasses
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  ef1be2a
- run_benchmark.py: select the primary DB beside dependency indexes
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  e99fd0c
- run_container_experiment.py: derive build jobs from Docker CPU budget
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  3c00500
- sha256: process complete input blocks without per-byte copies
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  committed
  56f2636
- perf(daemon): cache unchanged exact build fingerprints
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  842cfd7
- fix(mcp): copy normalized coverage scope strings
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  b9c43ab
- fix(mcp): expose advanced startup catalog to Codex
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  eb5e822
- fix(store): resolve active suffixes and bounded neighbors
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  10ee27c
- fix(mcp): read snippets from active overlay spans
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  1482958
- fix(mcp): return retry state while startup indexing runs
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  46029c8
- fix(mcp): scope freshness and name search count units
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  172c9d7
- fix(benchmarks): run measured Docker cohort under init
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  03b31e0
- perf(daemon): remove repeated image hashes and 500 ms watcher waits
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  b4873e9
- fix(cli): admit daemon tool calls without global transition
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  6e94770
- fix(mcp): carry list-change notices through daemon frontend
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  eab75cb
- fix(daemon): honor auto_index default at session start
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Commits on Jul 29, 2026
- fix(mcp): report zero returned rows in truncated query_graph replies
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  e881a2c
- cli.c: advertise the daemon subcommand in top-level --help
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  4d3fa48
- merge(upstream): combine main 560ad40d with API consolidation
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  dc1371a
- src/main.c: initialize memory only in supervised CLI workers
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  e755ec0
- fix(smoke): parse TOON tables and reap the Phase 15 FIFO
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  454d5be
- fix(mcp): separate TOON errors from response context
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  86bbb78
- fix(mcp): serialize context warnings without a leading comma
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  a9a7190
- test(windows): verify watcher uses the shared git.exe resolver
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  71614b3
- fix(runtime): validate fingerprint cache epochs and retain exact paths
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  c051d1e
- fix(runtime): admit cross-volume fingerprint caches
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  af8fc69
- fix(tests): exclude POSIX MCP helpers from MinGW
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  09f310d
- fix(cli): reject wrong-arch macOS Homebrew paths
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  6903a72
- fix(cli): honor explicit macOS install directories
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  a789887
- merge(cli): carry macOS PATH migration into consolidated API
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  514ae6f
- fix(mcp): suppress release notices for dev builds
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  1c87709
- fix(daemon): initialize active image fingerprint before comparison
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  25e45a6
- fix(lint): satisfy cppcheck 2.20 and LLVM 20 formatting
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  b7a0b7a
- fix(ci): remove stale suppressions and unsafe copies
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Commits on Jul 30, 2026
- merge(upstream): integrate f0c65fb2 release hardening
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- fix(benchmarks): emit clang-format-stable terminology header
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Commits on Jul 31, 2026
- fix(ci): close MCP stores and publish Windows files atomically
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  f4ef3a0
- .gitignore: adopt upstream's root-anchored /soak*/ and /memlab-* patterns
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  0a0aa69
- chore(upstream): merge main through 08f6d1d0
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  1acb3bb
- fix(cypher): enforce relationship-unique path matching
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  4b8b078
- perf(daemon): reuse application worker per connection
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  committed
  cd7bd48
- perf(mcp): reuse validated SQLite handle for query
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  6808941
- fix(benchmarks): emit indexed probes in self-dogfood runs
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  96b1d21
- test(mcp): isolate request-end allocator collection
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  9de6ab5
- benchmarks: retain request memory census for indexed probes
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  23f0cb9
- test(mcp): isolate request-scoped SQLite teardown
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- benchmarks: retain failed index worker logs
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  98db152
- fix(store): identify atomic publication failure stages
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  953f298
- fix(benchmarks): index archived worker-log facts
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  24b8897
- benchmarks: attribute indexed MCP server spans
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- benchmarks: split indexed request ownership costs
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- benchmarks: attribute index_status query phases
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- perf(store): materialize exact project graph statistics
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Commits on Aug 1, 2026
- test(cli): use UTF-8 filesystem observers
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Commits on Aug 2, 2026
Commits on Aug 4, 2026
Commits on Aug 8, 2026
- feat(api): combine exact publication, LSP, and workspace contracts
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  8455786
- feat(cli): ship SHA-256-pinned integration templates beside binaries
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  committed
  cd412fa
Commits on Aug 9, 2026
Commits on Aug 10, 2026
- feat(release): embed UI/templates and retain dependency indexing
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  committed
  32bc953
- fix(ui): binary-search assets and reject daemon port prefixes
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  3957880
- perf(extraction): make Python class filtering linear
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  8df9f9d
- src/cli/cli.c: retain released streamlined SessionStart hook
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  5504dcf
- notes/2026-08-09: record 4ed8d384 merge gates and bounds
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  8208add
- notes/2026-08-09: record installed binary 30ed57ee
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- merge: integrate upstream ad010b16 smoke composition
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  29c7a2f
- notes/2026-08-09: record ad010b16 workflow refresh
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  90a25f5
- src/{main,pipeline,ui}: satisfy clang-format checks
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- Merge upstream aa6d740a: report OS-truth diagnostics RSS
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- notes/merge assessment: record aa6d740a parent matrix
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- scripts/smoke-test.sh: match --standard rejection text
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  committed
  1a64a1f
- scripts/run-test-wave.py: enumerate dead-leader children natively
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  committed
  be24566
- application.c,mcp.c: construct daemon sessions without temporary SQLite stores
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  committed
  f0627b1
- tests/test_cli.c: exercise streamlined hook migration on Windows
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  committed
  a60199a
- notes/2026-08-09: record f062 daemon bounds and parent benchmarks
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  96cf097
- src/main.c: defer empty runtime-parent handling to bootstrap
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  add6e20
- notes/2026-08-09: record add6e20 Windows and install gates
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  8b6d321
- tests/test_py_lsp_bench.c: retain counters with upstream 30 s liveness backstop
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  committed
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- notes/2026-08-09: record caf81288 exact-parent benchmark matrix
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  committed
  9dd18e5
- tests/test_daemon_open_readiness*.py: resolve Windows .exe sibling
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  committed
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- tests/test_daemon_open_readiness.py: await Windows daemon process exit
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  committed
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- daemon.c,runtime.c: retain accepted slow-HELLO clients
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Commits on Aug 12, 2026
Commits on Aug 13, 2026
- fix(test-infra): stop on Windows ACL reset and grant failures
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  committed
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- tests/test_mcp.c: remove trace_path JSON trailing spaces
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  committed
  07255cf
- merge(upstream): retain managed spawn with bounded EAGAIN retries
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  committed
  f31d144
- internal/cbm/cbm.c: parse Perl beyond retired depth guard
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  committed
  3a2adbc
- src/foundation/subprocess.c: derive backoff from retry constants
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  committed
  7d4af17
- perf(lsp): collapse repeated Python scope-chain lookups
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  committed
  4d3a103
- internal/cbm/lsp/scope.*: inline complete binding lookup
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- notes/: remove local evidence files from the branch tip
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  committed
  c85018b
- merge(upstream): set Homebrew formula to v0.10.3 artifacts
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  committed
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- test(cli): require retired-flag compatibility warning
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  committed
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- merge(upstream): retain exact Windows process-owner validation
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  committed
  9b12c97
- merge(upstream): preserve fail-loud Cypher row budgets
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  committed
  f37b667
- merge(cli): route --skip-binary configs to running executable
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- merge(cli): select registry clients and reconcile Codex hooks
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- merge(startup): return MCP refusals without framing hooks
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- merge(config): route UI keys through the shared registry
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  committed
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- merge(config): self-heal orphan managed markers on removal
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Commits on Aug 18, 2026
- merge(upstream/main): integrate 4d7d9f11 as a superset of both parents
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Commits on Aug 19, 2026
- merge(upstream/main): integrate v0.10.8 as a verified superset
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  committed
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- fix(pipeline): preserve member import frontiers
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  committed
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- fix(pipeline): avoid incomplete parallel frontier resolution
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- fix(pipeline): retain all profiled log counters
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  committed
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- test_py_lsp_scale.c: confirm quadratic growth across two intervals
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  committed
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Commits on Aug 23, 2026
Commits on Aug 24, 2026
- fix(daemon): retain pre-admission bootstrap peers
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  committed
  42bbbd4

Commits

Commits on Jul 25, 2026

Commits on Jul 26, 2026

Commits on Jul 27, 2026

Commits on Jul 28, 2026

Commits on Jul 29, 2026

Commits on Jul 30, 2026

Commits on Jul 31, 2026