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Delta: doc-clean (calibrate-assessment-inventory)

MODIFIED Requirements

Requirement: Applier Applies Delete and Extract-Then-Delete Under the Tier Matrix

The patch applier SHALL support two new op kinds, delete and extract-then-delete. For both, immediately before applying, it SHALL re-run git ls-files <path> and a dirty check against that specific path — never trusting the cached report tier or rule claim — and SHALL apply the tier matrix from the lifecycle-deletion spec to decide whether the entry may proceed as auto or must be treated as confirm (already gated upstream by the clean skill). delete SHALL perform a git rm (recursive for a directory-rule aggregate entry) staged into the run's single hygiene commit. extract-then-delete SHALL first complete its generative extraction step (repo-durable via the existing live-read Sonnet distillation path writing into an ADR/CLAUDE.md/docs target, or cross-repo via /os-vault:write) and SHALL only perform the git rm once extraction has succeeded; both steps SHALL land in the same single hygiene commit, or, on extraction failure, neither SHALL be applied for that entry (skip, not a run-level hard failure, unless the failure matches an existing hard-failure trigger). When the extraction destination is the vault (the content physically leaves the repo), the op SHALL additionally append a pointer entry to the deleted file's per-directory extracted.md index (creating the file if absent), in the same atomic sequence — distill → /os-vault:write → append the pointer line → git rm — all staged into the same single hygiene commit, so there is no window where the doc is gone but undiscoverable. The pointer entry SHALL name the vault note, state why a future reader would follow it, and record the source filename and date. Repo-durable extraction targets (ADR, CLAUDE.md, docs) SHALL NOT produce an index entry — they are already discoverable in-repo.

Scenario: delete performs a true git rm at apply time

WHEN the applier applies a delete entry
THEN it re-verifies tracked/clean status via git ls-files and a dirty check, then performs a git rm staged into the single hygiene commit

Scenario: extract-then-delete only deletes after extraction succeeds

WHEN the applier applies an extract-then-delete entry
THEN it completes the extraction write (ADR/CLAUDE.md/docs or vault) first, and performs the git rm only after that write succeeds

Scenario: A failed extraction skips the delete for that entry

WHEN the extraction step of an extract-then-delete entry fails
THEN the delete is not applied for that entry, the entry is reported as skipped, and the run is not treated as a hard failure unless the failure matches an existing hard-failure trigger (applier exit 2, write error)

Scenario: Directory-rule aggregate delete removes the whole directory

WHEN the applier applies a delete entry whose path is a directory-rule aggregate entry
THEN it performs a recursive git rm removing the entire matched directory in one operation staged into the single hygiene commit

Scenario: A vault extraction leaves an extracted.md pointer in the same commit

WHEN an extract-then-delete entry extracts to the vault via /os-vault:write
THEN a pointer entry naming the vault note, the reason to follow it, the source filename, and the date is appended to the deleted file's directory extracted.md (created if absent), and the append, the deletion, and the index file are all staged into the same single hygiene commit

Scenario: A repo-durable extraction leaves no index entry

WHEN an extract-then-delete entry extracts into an ADR, CLAUDE.md, or docs target inside the repo
THEN no extracted.md entry is written — the residue is already discoverable in-repo

Scenario: A failed pointer append skips the delete

WHEN the vault write succeeds but appending the extracted.md pointer fails
THEN the git rm is not applied for that entry and it is reported as skipped, preserving the invariant that a doc is never gone but undiscoverable

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