C++ search - #210

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Commits on Jul 20, 2026

Commits on Jul 22, 2026

docs(mission-a): persist project5432 best-known trees + shared-floor result

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49c7fcf

Commits on Jul 24, 2026

Fix T-334: aggressive collapse flag reverted to conservative mid-search
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chore(red-team): record area 1 & 2 directed rounds (+ A1-OP-01 doc fix)

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chore(red-team): record area 3 directed round (T-335 filed)

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31b0627
chore(red-team): record area 4 directed round (T-336 P1 filed)

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9dbb30b
fix(T-336): per-worker ConstraintData copy in parallel_resample (data race)

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f951df5
chore(red-team): mark T-336 FIXED (f951df5a) in findings + log

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chore(red-team): record area 5 directed round (dry at opus)

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chore(red-team): area 6 dual-tier round (opus+fable calibration) — T-339..T-344

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a485581

Commits on Jul 27, 2026

feat(MaximizeParsimony): warm-start from a whole pool of trees

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chore(red-team): directed round on the warm-start pool diff (T-345..T-353)

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02de896
fix(ts_driven): don't credit the strategy bandit for warm-started replicates

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12bbb27
fix(MaximizeParsimony): root unrooted start trees before the binary check

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6fa9776
Merge fix/unrooted-start-normalization into cpp-search
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430c461
fix(red-team): correct area-6 cost note (tokens != cost) + record model-identity check

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cb87c4d
chore(red-team): area 7 rotation round (Shiny wiring) — T-354..T-361

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4a238ac
chore(red-team): close T-361 in place; record findings.md open-count

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d9a08c3
perf(iw): deepen the thorough/large ratchet to 48 cycles; couple to targetHits

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5640366
chore(red-team): tidy pass — archive 21 landed findings, reconstruct 5 deleted

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7359b16
Fix EasyTrees R-script download logging wrong thinning algorithm (T-354, T-360)

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d700bc9
fix(red-team): guard T-341/T-342/T-343 R-boundary validation gaps

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46c3806
chore(red-team): mark T-341/T-342/T-343 fixed in findings.md

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bf09116
chore(red-team): tidy follow-up — reconcile to-do.md, the coupled tracker

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1cc93a9
chore(red-team): archive T-354/T-360 — fixed mid-pass by d700bc95

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d14d4ea
chore(red-team): close T-346/T-348/T-350 (stale, already fixed in ee91dacc); fix T-351

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940e4af
chore(red-team): record T-351 fix commit hash in findings.md

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e134e42
fix(rcpp): T-339/T-337 — nThreads=0 auto-detect + parallel resample crash

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b148299
chore(red-team): close T-337, T-339 in place (b1482997)

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227d462
fix(search): saturate the no-improvement stop limit instead of overflowing int

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a94c16d
Fix T-340: normalize concavity in MaximizeParsimony() before dispatch

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dc00bcb
Merge remote-tracking branch 'local-treesearch/cpp-search' into claude/redteam-t346-cleanup
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59073a5
Rcpp crlf
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chore(red-team): close T-346/T-351 for real, reconciling with the concurrent tidy pass

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fix(rcpp): reapply T-339/T-337 fix lost in concurrent merge (ef54f473)

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ec3ce46
chore(red-team): trim provenance comments from the T-351 test move

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a10f5ee
Merge remote-tracking branch 'local-treesearch/cpp-search' into claude/redteam-t346-cleanup
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Merge branch 'fix/t340-concavity-normalization' into cpp-search
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Merge fix/t341-t342-t343-guards into cpp-search
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fix(shiny): red-team polish pass — T-356..T-359 (area 7)

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a2c63f7
Merge pull request #275 from ms609/claude/elegant-joliot-d637e5
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chore(red-team): area 8 round (sonnet/Sonnet 5) — T-362, T-363 filed

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e357e1b
Merge remote-tracking branch 'origin/cpp-search' into cpp-search
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e446e72
chore(red-team): tidy #2 — archive 6, clearing the last P2 from the open table

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897e31f
chore(red-team): tidy #2 follow-up — reconcile to-do.md's PR-named statuses

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b84a13c
chore(red-team): note why two adjacent tidy entries cite different last_focus

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c4ffb86
fix(red-team): T-362 — gate slow MaximizeParsimony() blocks, document mixed-tier exception

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6fc13b4
chore(red-team): recover the orphaned inapplicable-IW residual (area 9 → 10)

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9d3c656
feat(search): experimental flat replicate patience behind TS_STOP_PATIENCE

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4d8798b
refactor(PolEscapa): drop dead inappLevel assignment in LengthAdded()

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32435fd
docs(AdditionTree): correct the false "rooted on sequence[1]" return claim

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d3500aa
refactor(wagner): drop dead ew_score; correct the false "final_ is current" comments

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3c19b6b
chore(red-team): area 9 round (opus/Opus 5) - T-364..T-371 filed, P1 found

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f086f98
test(AdditionTree): pin the constraint test's seed; log the T-366 sibling lead

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9fc2b6e
chore(red-team): correct the area-9 log — 4 inline fixes, and why T-364 stayed filed

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db1fbfe

Commits on Jul 28, 2026

docs(wagner): note entropy scorer's weight-blindness is deliberate (T-371)
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fix(T-344): guard tip_states length in unpack_xform

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70ae4d5
docs(AdditionTree): clarify numeric concavity affects score only, not topology (T-369)

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0b5195d
Fix T-355: pair r$treeHash update with FirstHit's r$trees mutation
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c1c6b30
docs(red-team): T-335/T-338 tripwire comments at every cited hazard site
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fix(red-team): T-367 — delete unsound Phase-2 uppass in wagner_incremental_rescore

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Mark T-355 fixed in red-team findings log
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fix(T-366): score prune-reinsert backbone with fitch_score, not score_tree

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d94d76b
chore(red-team): file and close T-366 (prune-reinsert NA scoring mismatch)

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0354b68
fix(wagner): remove root-edge double-counting in random tree construction

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Merge branch 'cpp-search' into t370-wagner-edge-fix
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test(T-363): stop silently skipping R-level API tests on CRAN

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chore(red-team): archive T-370 as fixed

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0cd5c29
fix(red-team): T-365 — read PolEscapa index space after PrepareDataProfile

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chore(red-team): mark T-365 resolved; file T-372 (multiPhylo profile TreeLength)

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Merge branch 'cpp-search' into t370-wagner-edge-fix
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perf(wagner): T-368 — hoist constrained-start bookkeeping out of the per-edge loop

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chore(red-team): mark T-368 fixed; log the AdditionTree constraint lead under T-324

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03644e4
test(char-ordering): replace the tautological order-invariance test with a real differential

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5cffb18
Fix nocov block exclusion in rearrange.cpp (start not begin)
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ede9b3d
docs(AdditionTree): correct @return rooting claim, pin with a test

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e4ab114
chore(red-team): area 10 round (opus/Opus 5) - T-373..T-382 filed, four P1s in HSJ/XFORM

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RcppChurninator
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chore(red-team): settle the HSJ design question from the paper; T-376 is worse than filed

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ab56155
feat(search): ship stopPatience; deeper IW ratchet for sprint/default

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323a0da
fix(T-372): TreeLength()/LengthAdded() on uninformative profile characters
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chore(red-team): record T-372 fix commit SHA
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docs(search): state stopPatience's parallel-path limits; test them

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Merge origin/cpp-search into cpp-search

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fix: check for user interrupt inside tree_fuse()
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feat(search): intra-phase heartbeat; accept abbreviated strategy names

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2abe28e

Commits on Jul 29, 2026

chore(red-team): port the T-373/T-376 repros into the repo before they are swept

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4152e9a
chore(spelling): clear the 9 unknown words blocking the sense-check

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fix(T-380, T-381): Add dimension and invariant guards to prevent silent misscoring

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docs(red-team): record T-380 and T-381 fixes in findings.md

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886a1cb
Merge claude/t380-t381-guards: fix T-380/T-381 (Rcpp dimension guard + min_steps invariant guard)
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fix(collapse): stop reading stale local_cost for ratchet-zeroed blocks (T-382)
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Merge claude/t382-collapse-stale: fix T-382 (stale local_cost in collapse kernel)
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fix(tbr): key the NA optimum cache on the scoring regime; measure what the NA wall is

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35cfcdf
docs(red-team): settle the XFORM half of T-374 — keep the objective unrooted
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1aeba79
docs(red-team): correct T-374b's Q-C claim — incoherent, not refuted
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docs(red-team): T-374b's "blocker" is the already-filed T-377, not a new finding
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fix(xform): constrain -2 sentinel to known secondaries (T-379)

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docs(red-team): record T-379 fix commit SHA in findings.md

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bbcca1b
fix(T-364/T-370): enforce Wagner constraints through the split's complement

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7685bf0
fix(T-364): re-root the constrained Wagner tree so the split mapping can find it

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docs(red-team): close T-364/T-370; file T-384 (rooting-blind split mapping)

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fix(T-373): mode-aware total_words==0 bail for HSJ/XFORM search kernels

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docs(red-team): record T-373 fix (921500a9) in findings.md

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docs(red-team): tighten T-373 fix note after advisor review

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feat(tbr): add TBRParams::certify_unrooted, opt-in, plus the counters to gate it

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bench(na): floor-attainment panel for the certify_unrooted gate

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fix(driven): do not start a final certification past the maxSeconds budget

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docs(na-certify): record the panel job ids and the harvest order

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fix(claude): import AGENTS.md as @../AGENTS.md

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ecb754e
fix(T-370): verify the finished constrained Wagner tree instead of trusting the filter

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a84bb71
red-team(T-377): convergence-level reach measurement for the Fitch-only TBR/SPR screen
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docs(red-team): close T-377 on the convergence-level reach measurement
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Commits on Jul 30, 2026

fix(prune-reinsert): T-391 constraint compliance verify-and-revert

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1be2002
bench(T-364): three-arm battery — merged fix costs nothing; 1.43x reattributed

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fix(spr): T-390 constraint compliance verify-and-revert

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docs(red-team): record T-390 fix in findings.md

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test(AdditionTree): harden T-364 %in%-on-Splits assertions

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26d8d93
bench(na): certify_unrooted panel returns -- certification is OVER-SEARCH

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cb2f59c
docs(na-certify): scope the verdict -- the cap binds, and the loss is not uniform

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bench(na): second panel -- certification under the SHIPPED stopping rules

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docs(na-certify): the practical recommendation, and the targetHits coupling

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fix(T-384): rooting-agnostic constraint mapping via mask-or-complement

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docs(red-team): record T-384 fix, and the T-364 battery's reattribution

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041ccf0

Commits on Jul 31, 2026

fix(bench): no git operations inside an array task

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59ccd5c
Embrace `withr`
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29b62eb
Merge remote-tracking branch 'origin/cpp-search' into cpp-search
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feat(search): `effort` replaces `strategy`, as a RELATIVE offset

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ci: parallelise R dependency installation (Ncpus: 4)
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DIAGNOSTIC (will revert): drop MaxMin/Remotes to test P3M binary fallback
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12cfd57
Revert "DIAGNOSTIC (will revert): drop MaxMin/Remotes to test P3M binary fallback"
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897ba74
Revert "ci: parallelise R dependency installation (Ncpus: 4)"
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fix(effort): drop the invented rung-8 ceiling; double both budget knobs

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2d871b4
fix(ci): agent-check's arm64 leg was missing sense-check's R env vars
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docs: clear the three R CMD check items blocking sense-check

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21b0800
faster eg
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5a8a871
Update test-stop-patience.R
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Revert "fix(ci): agent-check's arm64 leg was missing sense-check's R env vars"
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2bcf201
test(stopPatience): drop a score assertion that only held at this machine's speed

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242bdd4
coord: queue the four live HSJ/XFORM P1s; record the T-385 repro on T-374
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7d4d255
coord: retract the T-374/T-385 MPT-set refinement -- my measurement was invalid
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T-385: reproduce the XFORM reported-score / TreeLength disagreement
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T-385: report the x-transformation score of the tree actually returned
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e6bc225
docs: regenerate a MaximizeParsimony example left stale by the effort rename
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coord: T-385 fixed; T-374's MPT-set residue CONFIRMED reachable
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T-385: share one dataset generator between the two diagnostic scripts
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T-385: pin the residue warning, guard the scripts' relative paths
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coord: T-385 -> PR #278 (stacked on #277)
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f13f0c3

Commits on Aug 1, 2026

Merge branch 'cpp-search' into claude/t385-xform-report-agreement
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Merge pull request #278 from ms609/claude/t385-xform-report-agreement
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bench(na): panel 2 returns -- targetHits escalation is pure cost (0 of 30)

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7b1b278
fix(ci): project .Rprofile shadowed ~/.Rprofile, killing all binary repos

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perf(ci): pin the dependency snapshot and drop LaTeX from sense-check

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df19a56
fix(hsj): translate token indices to state indices before comparison (T-375, T-376)
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perf(ci): ignore shinytest2 on Linux legs -- its chromium sysreq costs ~70 s/run

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test(hsj): add regression coverage that permutes contrast rows, not levels (T-375, T-376)
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docs: regenerate MaximizeParsimony.Rd (roxygen sync, pre-existing drift)
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317a9d5
docs(hsj-paper-oracle): caveat that check [3] passing here isn't a T-374 fix
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a29ff1d
probe(ci): time docker pull vs setup-r on arm64 (THROWAWAY -- delete after)

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probe(ci): self-trigger on push (workflow_dispatch needs the default branch)

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0fedb53
bench(na): retract the targetHits headline; panel 3 tests the actual hypothesis

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db5c657
probe(ci): remove container probe -- question answered

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perf(ci): ignore MaxMin on fast Linux legs -- ~67s/run, no infra needed
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test(ci): bump agent-check cache-version to 3 for a cold-cache MaxMin check
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revert(ci): drop throwaway cache-version bump used to verify MaxMin=?ignore
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coord: T-375/T-376 -> PR #280
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bench(vine): rule out embedding + NJ-decoder search for LS and for sectors

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eb2d540
test(hsj): add a value-level T-375 regression test (secondary "?" resolution invariant)
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4c96ec3
fix(ts_hsj_score): validate tip_labels/absent_state bounds
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33702c9
docs: promote T-374 caveat to printed output; log HSJ scoring change in NEWS
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ci: consume prebuilt MaxMin binaries from ms609/packages instead of ?ignore
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.build.timestamp
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Merge branch 'gha-ccache': fix CI dependency resolution + cut preliminaries

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39fcefc
fix(hsj): validate tip_labels/absent_state on the production search path too
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d2a2ebc
perf(hsj): restore per-character tie-break array sizing, reuse ctz64()
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bd2c74b
docs(hsj): fix review-flagged doc gaps -- NEWS accuracy, stale terminology, vignette
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fix(news): reword to avoid an unlisted possessive-acronym spelling flag
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465be29

Commits on Aug 2, 2026

Merge pull request #280 from ms609/feature/hsj-token-index-fix
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fix(hsj): stop charging the inapplicable state as a secondary mismatch (T-374)

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b5c52be
fix(hsj): root the secondary labelling canonically at tip 0 (T-374)

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test(hsj): cover T-374 rooting invariance and the reported-vs-returned symptom

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bench(na): hard-tail panel -- effort works, gating is refuted, notch 2 is inert

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1958f21
docs(hsj): record that HSJ is now rooting-invariant; sharpen the paper oracle

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docs(red-team): T-374 HSJ half fixed in PR #281

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c76638f
fix(hsj): free a secondary only where its primary CANNOT be present

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style(hsj): restore comment placement; drop the unused parent array
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Merge pull request #281 from ms609/feature/hsj-rooting-invariant-dp
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34eea58
docs(red-team): T-374 HSJ half merged as 34eea581

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11416f6
docs(na-certify): supersede the gating recommendation refuted by panel 3

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bbab0f7

Commits on Aug 3, 2026

red-team: area 10 round 2026-08-03 (opus/Opus 5) — 8 filed, T-377 reopened

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e56161a
docs(red-team): T-395/T-396 resolved — the paper decided both

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3d9ac49

Commits on Aug 4, 2026

docs(maxinfo): close the maximum-information / concave-branch line

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5ac9e28
red-team: area 11 round 2026-08-04 (opus/Opus 5) — 9 filed, 2 refuted

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03dc565
red-team: migrate findings to agent-issues/TreeSearch issue tracker

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20e0e0b
red-team: pin the findings.md recovery point to a tag, fix two stale figures

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45e5c88
chore: retire file-based coordination for the issue tracker

claude
authored and
ms609
committed
c8e6b6a
chore: delete dead coordination doc, trim AGENTS.md, complete the effort ladder

claude
authored and
ms609
committed
40ee662
chore(next-issue): drop issue-number examples, tighten to 111 lines

claude
authored and
ms609
committed
0af3ed0
Merge branch 'cpp-search' into chore/retire-file-coordination
ms609
authored
635a972
Merge pull request #40 from agent-issues/chore/retire-file-coordination
ms609
authored
99b79d8
perf(tbr): finish T-300 — incremental rescore for rerooting accepts too

ms609
and
claude
committed
ec9053e
red-team: area 12 round 2026-08-04 (sonnet/Sonnet 5) — 2 filed, coverage diff run

claude
authored and
ms609
committed
4964bf4
ci: give the Windows and macOS legs a MaxMin url:: reference

claude
authored and
ms609
committed
77158b9
ci: pin install-pandoc so pandoc auto-detect stops re-solving MaxMin by name

claude
authored and
ms609
committed
ca007d6
fix: validate presence and shape at the HSJ/XFORM bridge
ms609
committed
f96c81e
fix: enforce user constraints at the start-tree, pool-capture and collapse boundaries

ms609
and
claude
committed
4e6adae
docs: fix GHA dispatch recipe to use absolute script paths
ms609
committed
6a814a7
Merge pull request #49 from agent-issues/feature/hierarchy-guards
ms609
authored
b19d460
test(EasyTrees): let the dataset load settle before setting treeRange

ms609
and
claude
committed
e3c294d
Merge branch 'cpp-search' into claude/exciting-greider-977d08
ms609
authored
ea4d367
docs: use C:/ path style consistent with rest of AGENTS.md
ms609
committed
3917e94
Merge pull request #52 from agent-issues/claude/exciting-greider-977d08
ms609
authored
da88e53
fix(wagner): pass real min_steps to AdditionTree()'s Wagner build; note tip_ambiguous plane-0 behaviour

ms609
and
claude
committed
2dde491
branches: ["**"]
ms609
authored
73a0e87
Merge pull request #53 from agent-issues/ms609-patch-1
ms609
authored
93f489d
Merge branch 'cpp-search' into feature/shiny-debounce-wait
ms609
authored
b332720
fix: reject non-binary trees at the TreeState boundary

ms609
and
claude
committed
7c8c3ab
fix(docs): correct the false $score claim; tighten and extend min_steps tests

ms609
and
claude
committed
a9f872c
fix: address review findings on the constraint gates

ms609
and
claude
committed
8cfbf3b
Merge branch 'cpp-search' into feature/ci-maxmin-windows
ms609
authored
7faf23a
Merge pull request #45 from agent-issues/feature/ci-maxmin-windows
ms609
authored
f00478c
Merge pull request #48 from agent-issues/feature/shiny-debounce-wait
ms609
authored
2c59965

Commits on Aug 5, 2026

Merge branch 'cpp-search' into feature/multifurc-oob
ms609
authored
9d8696a
Merge branch 'cpp-search' into feature/wagner-docs
ms609
authored
8f66fe9
fix: make the constraint standard one thing, and say what it is

ms609
and
claude
committed
2397620
Merge branch 'cpp-search' into feature/redteam-area12
ms609
authored
4b0f740
Merge pull request #44 from agent-issues/feature/redteam-area12
ms609
authored
174f65b
fix(hsj): skip the childless case before pointing into co.kids

ms609
and
claude
committed
ca5c1c0
Merge branch 'cpp-search' into claude/treesearch-issue-38-8103cc
ms609
authored
7519527
docs(red-team): move the skill in-repo, GitHub-issues only; close the routing and scope gaps

ms609
and
claude
committed
bd0f70d
fix(red-team): the skill stays user-level — this branch carries rotation state only

ms609
and
claude
committed
76cec86
docs: record the local assertions-build route for HSJ/XFORM bounds bugs

ms609
and
claude
committed
5928f7f
review(tbr): make n_reroot_accepts witness the arm it guards

ms609
and
claude
committed
44924e5
review: correct the mechanism claim; land the CanonOrder evidence script

ms609
and
claude
committed
38ded4d
docs(news): name the mechanism that aborted, not the workflow that stopped

ms609
and
claude
committed
c054e3f
Merge pull request #55 from agent-issues/feature/wagner-docs
ms609
authored
38115e4
Merge pull request #50 from agent-issues/feature/multifurc-oob
ms609
authored
3d3e3c2
Merge pull request #47 from agent-issues/claude/treesearch-issue-38-8103cc
ms609
authored
1d55546
fix(gitignore): narrow /.agent* to /.agent-* to stop matching .AGENTS/ on Windows

ms609
and
claude
committed
72e25b7
Merge pull request #74 from agent-issues/feature/gitignore-agents-collision
ms609
authored
88cf860
Merge branch 'cpp-search' into feature/constraint-holes
ms609
authored
dfbd2d2
Merge pull request #73 from agent-issues/feature/hsj-oob-read
ms609
authored
d030640
Merge pull request #59 from agent-issues/feature/constraint-holes
ms609
authored
f9c4e63
Merge pull request #57 from agent-issues/claude/red-team-skill-github-4853c6
ms609
authored
53f3dc5
Merge pull request #284 from agent-issues/cpp-search
ms609
authored
38a6ffd

Commits on Aug 6, 2026

feat(effort): scale the MPT-enumeration ceiling, not poolMaxSize

ms609-agent
and
claude
committed
a9e2634

Commits on Aug 11, 2026

Merge pull request #285 from ms609/feature/enum-pool-ceiling
ms609
authored
8b6e502