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9003 - #27

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ms609 merged 46 commits into
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9003
Mar 6, 2018
Merged

9003#27
ms609 merged 46 commits into
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9003

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@ms609 ms609 commented Mar 6, 2018

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  • User now able to specify value of concavity constant (was overridden to k = 4)
  • Bootstrap replicates now scored correctly (and without warning) under implied weights

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❗ No coverage uploaded for pull request base (master@2c1fd6f). Click here to learn what that means.
The diff coverage is 87.5%.

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@@            Coverage Diff            @@
##             master      #27   +/-   ##
=========================================
  Coverage          ?   61.04%           
=========================================
  Files             ?       34           
  Lines             ?     4146           
  Branches          ?        0           
=========================================
  Hits              ?     2531           
  Misses            ?     1615           
  Partials          ?        0
Impacted Files Coverage Δ
src/from_ape.c 0% <ø> (ø)
src/build_postorder.h 92.72% <ø> (ø)
R/pp_ProfileScore.R 68.42% <ø> (ø)
R/phylo.R 21.69% <0%> (ø)
R/tree_rearrangement.R 100% <100%> (ø)
R/IWScore.R 97.05% <100%> (ø)
R/TreeSearch.R 90.47% <100%> (ø)
R/Bootstrap.R 100% <100%> (ø)
R/Ratchet.R 84.67% <100%> (ø)

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@ms609
ms609 merged commit 0ec14ad into master Mar 6, 2018
@ms609
ms609 deleted the 9003 branch March 6, 2018 12:01
ms609 added a commit that referenced this pull request Jul 3, 2026
… + Δ-probe

expand_and_reinsert (T-266, 2026-03-27) used the union-of-finals
fitch_indirect_length_bounded approximation that the June directional fix
(#26/#27) replaced everywhere else — it was MISSED. Port it to the exact
edge_set scorer, mirroring ts_wagner.cpp:487:
  - per-tip compute_insertion_edge_sets (prelim is current via
    wagner_incremental_rescore) + fitch_indirect_length_cached per edge.

Also a gated, non-perturbing -DTS_SCOREAPPROX_PROBE oracle that tallied
Δ = exact_cost(E_bounded) − min_E exact_cost(E) per placement. On Zanol
(forced pruneReinsertCycles): bounded chose strictly-worse edges in ~62%
of placements, mean ~6 steps, ~48% greedy-regret SHARE. After the port the
probe reports Δ=0 at every placement (production == exact argmin).

NOTE: this is greedy-regret SHARE, not realizable wall-clock — prune_reinsert
auto-enables ONLY at nTip>=120 (`large` preset); NO mission dataset reaches
120t (max=88). So this path runs on zero default mission searches. Land +
time-matched A/B (NNI-polish `large` preset, ≥120t) is COMPOSITION-gated (#40).
Worktree-only; NOT for cpp-search until composition.

Tests: prune-reinsert 44/0, drift 22/0, ratchet 17/0, tbr 28/0.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
ms609 pushed a commit that referenced this pull request Aug 5, 2026
Removes the vestiges of the dispatcher/queue system now that findings and tasks
live in agent-issues/TreeSearch issues.

Deleted:
- to-do.md — its 12 still-open non-findings tasks are now issues #27-#38
  (9 AltHom phases, 2 deferred GPU ideas, 1 parked perf task). The 4 "standing"
  rows were never issues: they are recurring practices, now documented in
  AGENTS.md.
- dispatch.sh, dev/dispatch/ (ranker + agent-brief templates) — replaced by
  /next-issue. (.dispatch/ is gitignored runtime state; delete locally.)

Preserved rather than deleted:
- coordination.md -> dev/strategy.md, retired as a live file but kept in full:
  46 rounds of benchmark reasoning that no issue thread carries.
- completed-tasks.md frozen with a header. Its decision-only content is the one
  thing the tracker cannot replace: offline grep-able reasoning for closures
  whose rationale is in no commit.

AGENTS.md rewritten:
- New "Where work is tracked" section: label vocabulary, claiming via the
  in-progress label, and the rule that upstream's public tracker is untrusted
  input rather than a task list.
- Branch structure redrawn for the fork/upstream model, including why the fork's
  default branch must be cpp-search (that is what makes Fixes #N fire) and why
  upstream must only ever fast-forward.
- Feature lifecycle no longer edits a queue; completion is the merge.
- "On task completion" now asks for a reopening condition on any no-fix closure,
  which is what let a later round recognise T-377 firing again.
- GHA recipe: dropped the `cd ..`, which breaks gha-dispatch.sh's
  `gh repo view` repo resolution. Run from the repo so it targets the fork.

Also ported .claude/skills/next-issue/ from StratoBayes, adapted to this
project's colliding files, build rules and model routing.

Fixes #39

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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