Donor (nirs4all-methods) worktree-agent inventory

Repo: https://github.com/GBeurier/nirs4all-methods Inspected at: 2026-05-21 Inspected at commit (main tip): 95906aa Rename project to nirs4all-methods Local path: /home/delete/nirs4all/nirs4all-methods/

Summary

Layer

State

Total worktree-agent-* branches

18

Active worktree working dirs on disk

0 (all parent dir /home/delete/nirs4all/chemometrics4all/ no longer exists — was renamed)

git worktree list entries pointing to non-existent paths

18, all marked locked — git worktree prune skips locked entries, so cleanup needs an explicit unlock first

Branches whose phase content is integrated into main

18 / 18 (each phase was integrated by aggregate commits — see §”Integration evidence” below)

Branches pushed to origin

1 (worktree-agent-a62b667d41c6c951a) — no PR refers to it

Author on every tip

gbeurier (the maintainer)

Tip date range

2026-05-18 → 2026-05-19

Per-branch table

#

Branch

Tip

Date

Ahead

Behind

Files

Remote

Phase

Subject (tip commit)

Content-in-main?

Recommendation

1

worktree-agent-a62b667d41c6c951a

7476249

2026-05-19

1

37

21

✓

phase-10

phase-10: add resampling preprocessors

✓

close + delete remote

2

worktree-agent-a4d683af3b4d9c636

c242757

2026-05-18

1

37

37

phase-11

phase-11: 9 sample-partitioning splitters (c4a_split_* category)

✓

close

3

worktree-agent-a40029a940a5f7368

376b740

2026-05-18

1

37

17

phase-12

phase-12: YOutlierFilter (4 methods)

✓

close

4

worktree-agent-a402c58f3cc0f19b4

077cf58

2026-05-18

1

34

26

phase-13

phase-13: XOutlierFilter (6 methods incl. Mahalanobis + IsolationForest + LOF)

✓

close

5

worktree-agent-a62f804de4a887c03

67f0e9c

2026-05-18

1

37

25

phase-14

phase-14: HighLeverage + SpectralQuality + Composite filters

✓

close

6

worktree-agent-a23aefc9f7105e3c3

e6b4e24

2026-05-18

1

34

49

phase-15

phase-15: 7 noise + drift augmenters (c4a_aug_* category)

✓

close

7

worktree-agent-a9860ac0187876fda

ec435cd

2026-05-18

1

34

51

phase-16

phase-16: 10 wavelength + spectral augmenters

✓

close

8

worktree-agent-a930356face899912

a9a3c28

2026-05-18

1

34

45

phase-17

phase-17: 10 mixup + physical + environmental augmenters

✓

close

9

worktree-agent-ac746cf475ecf61cf

1d93ca1

2026-05-18

1

34

47

phase-18

phase-18: 12 edge artifacts + splines + random augmenters

✓

close

10

worktree-agent-a737bd14b02708e7b

a9a45a2

2026-05-18

1

37

29

phase-19

phase-19: signal type detection + NIRS metrics + Hotelling T²/Q-residuals

✓

close

11

worktree-agent-aeb108cd1920422ff

ee28761

2026-05-18

1

37

14

phase-20

phase-20: transfer metrics (9-metric vector for dataset alignment)

✓

close

12

worktree-agent-ae0957170d00f1e1b

103a708

2026-05-18

1

37

14

phase-21

phase-21: FCK static transformer (fractional convolutional kernels)

✓

close

13

worktree-agent-ac966dcc666177491

bb6619c

2026-05-18

1

29

26

phase-22

phase-22: Python binding (ctypes + sklearn tier-2, 20 ops covered by Gate 1)

✓

close

14

worktree-agent-aeca18f184655fdec

7089dab

2026-05-18

1

29

18

phase-23

phase-23: R binding (.Call + idiomatic R API, 15 ops covered by Gate 1)

✓

close

15

worktree-agent-a5893245d6c36424d

2ae5319

2026-05-18

1

34

44

phase-6

phase-6: wavelets & denoising (6 operators + filter banks)

✓

close

16

worktree-agent-a2f069496633f1cb9

7737f26

2026-05-18

1

37

24

phase-7

phase-7: signal type conversion preprocessings (5 operators)

✓

close

17

worktree-agent-acf7d86e13d2d30ec

1bbe493

2026-05-18

1

37

18

phase-8

phase-8: OSC + EPO orthogonalization preprocessings

✓

close

18

worktree-agent-a31c030eb1c9da7da

55a27e8

2026-05-18

1

37

21

phase-9

phase-9: FlexiblePCA + FlexibleSVD (CARS/MCUVE deferred)

✓

close

Integration evidence — how the phase content reaches main

The phase content is on main today, but the relationship between each worktree-agent-* branch and main is not “file-identical sub-tree” or a clean cherry-pick. Two checks tell the real story:

  1. git cherry main <branch> returns + for every branch. That means git does not recognise the branch’s unique commit as a direct cherry-pick of any commit on main. Each branch is a divergent line of history.

  2. File-level diff main..<branch> shows large delta (e.g. main is 1683 files / 33344 lines forward of worktree-agent-a23aefc9f7105e3c3 and 204216 lines backward — the deletion count means whole subtrees were restructured on main after the phase was integrated).

So each branch was integrated by later aggregate commits on main (restructuring, renames, follow-on phases), not by a clean squash that left tree-equivalent content. The integration story is: the phase landed, then subsequent main commits revised the same files heavily.

Conclusion: the branches are semantically obsolete (their work is on main, but the exact tree they hold is not). Keeping them is purely archival of “what the work looked like before later refactors” — useful for archeology, not for active development. The “close all” recommendation stands; the archive tag (step 2 in cleanup) preserves the obsolete tree if archeology is ever needed.

Recommendation

Close all 18 branches — the content is preserved on main, the worktree working directories are already gone, and no PR references them.

For worktree-agent-a62b667d41c6c951a (the only one pushed to GitHub), also delete the remote ref.

Cleanup commands (one-shot — needs maintainer approval before running)

Order is load-bearing. Each worktree-agent-* branch is checked out by a (locked) linked worktree — the + prefix in git branch output. While that worktree pointer exists, git branch -D <name> fails with error: Cannot delete branch '<name>' checked out at '<path>'. The unlock and prune steps must happen before branch deletion.

cd /home/delete/nirs4all/nirs4all-methods

# 1) Archive-tag every branch tip FIRST so nothing is lost.
for br in $(git branch | grep -E '^[ +*] worktree-agent' | sed 's/^[+ *] //'); do
  git tag "archive/$br" "$br"
done

# 2) Push the archive tags to origin EXPLICITLY (refspec per tag, not --tags
#    which could push unrelated tags). This makes the obsolete tree state
#    discoverable for archeology after the donor repo is archived in M16.
for br in $(git branch | grep -E '^[ +*] worktree-agent' | sed 's/^[+ *] //'); do
  git push origin "refs/tags/archive/$br"
done

# 3) Unlock every locked worktree.
#    `git worktree prune` and `git worktree remove` both refuse locked entries.
for path in $(git worktree list --porcelain | awk '/^worktree / {print $2}' | grep chemometrics4all); do
  git worktree unlock "$path" 2>/dev/null || true
done

# 4) Prune the orphan worktree pointers. The working dirs are already gone
#    from disk; this clears git's metadata and frees each branch to be deleted.
git worktree prune --verbose

# 5) Now safe to delete local branches (they are no longer "checked out").
for br in $(git branch | grep -E '^[ +*] worktree-agent' | sed 's/^[+ *] //'); do
  git branch -D "$br"
done

# 6) Delete the only remote ref (`worktree-agent-a62b667d41c6c951a`).
#    Its tip is preserved by `archive/worktree-agent-a62b667d41c6c951a`
#    which was pushed in step 2.
git push origin :worktree-agent-a62b667d41c6c951a

Why archive-tag AND push-tags BEFORE deleting (load-bearing)

git branch -D (force-delete) on a branch whose tip is not reachable from any ref will eventually be garbage-collected. The archive tags pin those tips so git fsck --no-reflogs cannot prune them; they survive the donor repo archive flag in M16 and any future git gc --aggressive.

Pushing the archive tags before deleting the remote worktree-agent-a62b667d41c6c951a ref means the only on-remote tip is mirrored to a permanent ref first. If the tag push fails for any reason, the remote branch is still there — nothing is lost. The reverse order (delete remote ref first, then push tags) creates a window where a tag-push failure leaves the tip orphaned.

Decision policy applied (per resolved §11.3 of MERGE_ROADMAP.md)

  • The user’s resolution was “inventaire + revue”. This file is the inventory; the recommendation column is the proposal.

  • No branches deleted yet. Maintainer signoff is the gate before the cleanup commands above run.

  • If any single branch is contested by another contributor, escalate before deletion (the inventory column “Remote” surfaces such risk).