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 980 commits into

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ahundt:api-consolidation

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Commits on Jul 22, 2026

refactor(config): derive limits with shared stringify macro
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c32123e
feat(benchmark): emit versioned experiment fact tables
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4950cc7
config: Set automatic dependency-source indexing disabled by default
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79ae943
benchmark: Pin dependency-source indexing profiles and isolated environments
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8d415b9
fix(benchmark): reject boolean numeric experiment fields
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d08ecbe
fix(depindex): bound invalid automatic dependency limits
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8d0816d
fix(mcp): reject integer arguments outside int range
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d030c8f

Commits on Jul 23, 2026

feat(indexing): select correctness-first reindex policies
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1c68799
fix(benchmarks): isolate config spelling probes
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b2fa24a
feat(benchmarks): bind v2 facts to terminology registry
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6eb10de

Commits on Jul 24, 2026

feat(benchmarks): derive contract-bound comparison facts
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c1e2ba1
refactor(benchmarks): consolidate canonical assets under benchmarks
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603e516
fix(benchmarks): restore upstream scripts and resolve retained plans
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486a363
fix(depindex): bound unlimited discovery allocations
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9eb20b3
refactor(benchmarks): hoist report helpers and harden process cleanup
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dc31d0f
fix(pipeline): preserve fresh re-export metadata in exact deltas
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19a4dec
fix(cli): list check_index_coverage in main help
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f29c105
fix(cli): normalize retained dependency limits in hook guidance
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138d287
fix(benchmarks): omit duplicate minimal-indexing experiment cells
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36698e5
fix(docs): name the active minimal-indexing benchmark profile
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e8398d5
style(benchmarks): format report test entry-point paths
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ea422a5
fix(depindex): enforce and report automatic dependency bounds
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e837baa
docs: remove stale Go wrapper and MCP tool count
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8ab7120
fix(pipeline): reject weak calls to data symbols
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fdce258
style(mcp): restore hidden-tool schema block indentation
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0d8d60c
test(pipeline): reject data-target subscript call evidence
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7e10bae

Commits on Jul 25, 2026

feat(merge): combine daemon runtime with graph coverage
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a15031e
fix(tests): terminate Windows subprocess skip macro
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2f4b28a
fix(subprocess): classify zombie-only groups after force reap
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d5637d9
fix(depindex): define manifest table once
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6a5ba5c
fix(build): analyze tests with gated API seams
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36533ba
fix(tests): skip fork latency canary under TSan
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132db9c
fix(build): scope Guard Malloc to owning suites
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8144bd3
test(pipeline): preserve graph on unreadable coverage
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cd812d0
fix(metadata): persist complete dirty-file observations
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afd2d2c
refactor(git): execute repository queries with literal argv
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d04e493
test(c-lsp): resolve xxhash fixture from runner image
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9c0e2b1
test(py-lsp): measure scale guard with process CPU time
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1287e37
fix(platform): reject truncated environment values
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e59b923
fix(mcp): use configured auto-index admission helper
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7067f57
fix(build): give analyzer the test harness include path
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0d8aede
fix(build): propagate Clang analyzer failures
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369ac89
build(test-syntax): reuse the real C test flags
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d1c7795
test(mcp): keep environ declaration POSIX-only
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e06d2a2
fix(build): preserve leak command status under /bin/sh
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fecde17
refactor(json): share exact escaped-length accounting
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3a0aa48
refactor(config): share query output byte definitions
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fcab139

Commits on Jul 26, 2026

fix(cypher): separate output caps from working budgets
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8cad620
fix(depindex): rank from every project import
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41d60e9
fix(depindex): stream every project import edge
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7107418
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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879a53c
fix(store): retain every file-tree directory
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c0fd3fa
fix(store): omit prefix clusters beyond node budget
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a752956
fix(cypher): bind variables beyond inline storage
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3851cfe
fix(pipeline): scan complete cross-repo edge streams
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319fb7a
refactor(config): share search preview defaults
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0c41e7a
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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707c0ed
test(main): select env-filtered suites from canonical registry
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838626f
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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619d3d3
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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1cd3466
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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89ea077

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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c6e4b6f
fix(benchmarks): record Makefile compiler identity
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7dac25f
fix(benchmarks): record self-dogfood comparison manifests
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34a4740
fix(cli): stop advertising deprecated inline JSON
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f847c98
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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a4676e4
fix(mcp): parse current search_graph JSON in smoke harness
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5d3ac0c
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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638186b
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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0590236

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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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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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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6d689bd

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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459351f

Commits on Jul 30, 2026

merge(upstream): integrate f0c65fb2 release hardening
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1c1d3ca
fix(benchmarks): emit clang-format-stable terminology header
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77bcddd

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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cd7bd48
perf(mcp): reuse validated SQLite handle for query
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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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benchmarks: retain request memory census for indexed probes
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test(mcp): isolate request-scoped SQLite teardown
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benchmarks: retain failed index worker logs
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fix(store): identify atomic publication failure stages
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fix(benchmarks): index archived worker-log facts
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benchmarks: attribute indexed MCP server spans
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91fb439
benchmarks: split indexed request ownership costs
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142cd9b
benchmarks: attribute index_status query phases
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e032157
perf(store): materialize exact project graph statistics
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cfb1b10

Commits on Aug 1, 2026

test(cli): use UTF-8 filesystem observers
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b465147

Commits on Aug 2, 2026

Commits on Aug 4, 2026

Commits on Aug 8, 2026

Commits on Aug 9, 2026

Commits on Aug 10, 2026

feat(release): embed UI/templates and retain dependency indexing
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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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notes/2026-08-09: record 4ed8d384 merge gates and bounds
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notes/2026-08-09: record installed binary 30ed57ee
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1f8ccb7
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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a2e019f
Merge upstream aa6d740a: report OS-truth diagnostics RSS
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notes/merge assessment: record aa6d740a parent matrix
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941ced9
scripts/smoke-test.sh: match --standard rejection text
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1a64a1f
scripts/run-test-wave.py: enumerate dead-leader children natively
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be24566
application.c,mcp.c: construct daemon sessions without temporary SQLite stores
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f0627b1
tests/test_cli.c: exercise streamlined hook migration on Windows
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notes/2026-08-09: record f062 daemon bounds and parent benchmarks
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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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caf8128
notes/2026-08-09: record caf81288 exact-parent benchmark matrix
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9dd18e5
tests/test_daemon_open_readiness*.py: resolve Windows .exe sibling
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tests/test_daemon_open_readiness.py: await Windows daemon process exit
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f7f9d96
daemon.c,runtime.c: retain accepted slow-HELLO clients
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8fa5df2