prune

Systematically evaluate the thesis portfolio; recommend keep / upgrade / kill. Be ruthless — cognitive overhead of tracking weak positions has a real cost.

Design rationale in .claude/skills/prune/RATIONALE.md (§N.M anchors).

Execution context — split delegation (2026-07-08, MANDATORY)

/prune splits across the subagent boundary because it has a read-heavy analysis half (~42 full-thesis reads) and a mutation half gated by mandatory user approval. A subagent cannot obtain mid-run user confirmation, and destructive edits must stay in the main thread. So:

ANALYSIS HALF — delegate to ONE Agent subagent (subagent_type: general-purpose, run_in_background: false). The subagent runs Phase 0.0.2 (rename-marker check) + Phase 0 (unsynced-research scan) + Phase 1–4 under a read-only lock (.vault-lock.readonly per preflight Procedure 1; it performs no writes). It reads every candidate thesis, does the two-pass triage and per-candidate assessment, and its final message returns EXACTLY:

Mental Models reading gate MUST cross the delegation boundary (MANDATORY — CLAUDE.md; _shared/mental-models-section.md). The subagent does NOT inherit CLAUDE.md, so the agent prompt MUST embed this gate verbatim: "Before judging any thesis for upgrade/monitor/close, read Mental Models/Generalist - Overview.md + the matching Mental Models/Industry - X.md/Lens - X.md for the candidates' sectors. Apply the READING PROTOCOL — a kill/keep call is a hypothesis; run the base-rate adversarially (stale ≠ wrong; a quiet thesis may still be right); read each candidate's own ## Mental Models disconfirming check before recommending closure."

1. A pre-flight status: either PREFLIGHT-OK, or PREFLIGHT-BLOCKED: <rename-marker | first-run | unsynced-research> with the details/file list the main thread needs to surface. Override contract: if the invoking prompt contains a line PREFLIGHT_OVERRIDE: <unsynced-research | first-run> approved YYYY-MM-DD, treat the corresponding Phase 0 gate as user-resolved — report the condition as a one-line warning (⚠️ Phase 0.B: 145 unsynced files — proceeding under user override YYYY-MM-DD) and CONTINUE to Phases 1–4 instead of returning PREFLIGHT-BLOCKED. (rename-marker is NEVER overridable — it is a hard-block per preflight Procedure 2.)

Recursion guard — the agent prompt MUST also embed verbatim: "You are the EXECUTOR of this analysis run, not a coordinator: do NOT re-delegate any part of this work to further Agent calls. Perform all reads and analysis yourself and end your final message with the three return items." 2. The full Phase 4 report (Recommendation Table + Portfolio Stats + Attention Allocation) — rendered verbatim by the main thread. 3. A compact execution plan the mutation half consumes without re-deriving analysis:

• closures: list of (ticker, filename, conviction_at_closure, one-line rationale)
• upgrades: list of (ticker, filename, old→new conviction, justification, Log line)
• affected_sectors: list of (sector_note_path, match_confidence, log_message) from _shared/sector-resolution.md The subagent releases its read-only lock before returning.

MUTATION HALF — main thread only. The main thread:

• If the subagent returned PREFLIGHT-BLOCKED, surface the corresponding Phase 0.0.2 / Phase 0.A / Phase 0.B prompt and get user resolution. On "proceed anyway" approval for unsynced-research or first-run: re-invoke the analysis subagent with the SAME prompt plus the line PREFLIGHT_OVERRIDE: <condition> approved YYYY-MM-DD — the override crosses the delegation boundary and the fresh subagent proceeds past that gate (this closes the dead end where approval changed no vault state and the re-invoked subagent re-blocked on the same condition forever). For rename-marker, there is no override — the user must finish/repair the rename first, then re-invoke normally.
• Render the Phase 4 report verbatim, then run the Phase 5 approval gate and the entire Phase 5 Atomic Batch (Stages 1–5) exactly as specified below — unchanged. Acquire the vault-wide write lock here (Phase 0.0.1), at the start of Phase 5, not before. Re-read only the approved-for-mutation theses + affected sector notes (bounded set — never the full portfolio) before editing them, per the read-before-write rule.

Why the lock moves: the long read phase now runs under a read-only lock inside the subagent (narrower, non-blocking to other readers); the vault-wide write lock is held only for the short mutation window in the main thread. All Phase 5 snapshot/manifest/graph-invalidation/_hot.md machinery is untouched. Why not full delegation: the Phase 5 approval gate and destructive edits require the main thread. Why not frontmatter context: fork: that mechanism was reverted 2026-06-07 (unrendered-stdout blank panel); Agent-tool delegation returns the report as a tool result the main thread re-emits. Revert path: delete this section; the skill then runs entirely inline (report renders, ~42 reads land in main context).

Scope Resolution

Parse $ARGUMENTS. Arguments can combine (e.g., /prune semiconductors stale):

• Sector (e.g., semiconductors): evaluate theses with matching sector: frontmatter only.
• Flag filter (pre-filters before full reads):
  • stale → last Log entry >60 days old
  • low → conviction: low
  • draft → status: draft
  • monitoring → status: monitoring
• No arguments / empty: evaluate all theses.

Pre-filtering grep on frontmatter avoids loading 39+ files when only a subset matches.

Phase 0.0: Pre-flight

0.0.1: Acquire vault lock

Under split delegation (see Execution context): the analysis subagent holds a read-only lock (.vault-lock.readonly) for Phase 0.0.2 + Phase 0 + Phase 1–4; the main thread acquires the vault-wide write lock here at the start of Phase 5, immediately before the first destructive stage, and releases it in the final Phase 5 block. (Inline-fallback mode without delegation: acquire the vault-wide lock at the very start as the original single-lock flow.)

vault-wide scope per .claude/skills/_shared/preflight.md Procedure 1. Timeout 15 min (large portfolios are slow). Capture token, verify (Procedure 1.5) every block, release in final.

0.0.2: Vault-wide rename marker check (§8)

Glob .rename_incomplete.*. ANY marker → hard-block (all-or-nothing — §8.1):

❌ In-flight rename repair detected — /prune would compound split state.

Markers found:
  - .rename_incomplete.TICKER1 ([new_name from marker])
  - ...

/prune closes, upgrades, and reshapes sector notes — each operation keyed to
the CURRENT thesis filename. Any affected thesis mid-rename would leave
inbound references split across old and new names.

Complete or abandon all in-flight renames first:
  /rename TICKER "[new_name]"    # per marker
  OR
  rm .rename_incomplete.TICKER   # accept broken wikilinks

Wait for user resolution. Do NOT proceed.

Phase 0: Check for Unsynced Research (§7)

Three states based on .last_sync and find -newer outcome:

Phase 0.A: .last_sync absent — first-run state (B4 fix)

If .last_sync does not exist at vault root, the next /sync will treat the entire vault as first-run (epoch placeholder, every file matches find -newer). Proceeding with /prune in this state means closures/upgrades are evaluated against thesis state that may not yet reflect the most recent research notes. Hard-prompt before continuing:

⚠️ First-run state detected — .last_sync is absent at vault root.

The vault has either never been synced, or .last_sync was deleted (manually,
accidentally, or via `git restore` that wiped it). The next /sync (any mode)
will treat this as a first-run and re-process every file in the vault.

/prune evaluates closure candidates by reading thesis state directly, but the
thesis state in a first-run vault may not yet reflect insights from research
notes that haven't propagated yet. Running /prune now risks closing or
upgrading theses based on incomplete evidence.

Recommended: run /sync first to establish the watermark and propagate any
pending research, then re-run /prune.

Options:
  (a) Cancel — exit /prune. Run /sync, then re-invoke /prune.
  (b) Proceed anyway — accept the risk that recommendations may not reflect
      the latest research. Use only if you have already verified that no
      research notes are awaiting propagation.

Confirm (a/b):

Do NOT proceed without explicit user confirmation. Decline → exit and suggest /sync. Approve → continue to Phase 0.B (which will report no changed files since the watermark is missing).

Phase 0.B: .last_sync present — unsynced-research scan

find Research/ Theses/ "Macro & Technology/" Sectors/ -newer .last_sync -name '*.md' 2>/dev/null

Changed files found → warn before proceeding:

⚠️ Unsynced research detected ([N] files modified since last /sync):
  [list]

Running /prune before /sync risks archiving theses before recent research insights
have been propagated. Recommended: run /sync first, then re-run /prune.

Proceed anyway? (y/n)

Do NOT proceed without explicit user confirmation. Decline → stop and suggest /sync.

Phase 1: Identify Candidates (Two-Pass Triage — §6)

If scoped: read only matching theses in full (typically small — skip two-pass triage).

If unscoped — Pass 1 lightweight scan (parallel full Reads):

Issue all thesis Reads as a single parallel tool-call batch — one message with ~42 Read invocations, all in full, landing in one round-trip. Do NOT serialize, and do NOT section-target at the tool level. The LLM sees every thesis body in full so subtle weakness signals outside the triage sections (e.g., a contradiction between Bull Case and recent Log entries, a Non-consensus Insight that's been quietly invalidated by newer research) aren't filtered out before the triage LLM reasons over them.

Triage focus prioritizes frontmatter + Related Research + Catalysts + Log (the mechanical flag inputs), but full-file context is kept intentionally — /prune is about spotting quietly-dead theses, which sometimes requires reading between the sections.

Apply flag criteria:

Flag	Criteria	Source
🟡 Low conviction	conviction: low	frontmatter
🟡 Monitoring	status: monitoring	frontmatter
🔴 Stale	Last Log >60 days old	Log dates
🔴 Very stale	Last Log >120 days old	Log dates
🟡 Thin research	<3 research notes linked	Related Research
🟡 Draft limbo	status: draft with only 1 Log entry	frontmatter + Log count
🟡 Orphaned from sector	Not in Sector Note	deferred to Pass 2
🔴 No catalyst	Catalysts empty or all dates past	Catalysts section

Also flag: high-conviction theses with stale research (last Log >90 days despite conviction: high).

Pass 2 — deep read flagged candidates:

• Each flagged → proceed to Phase 2 (full note read).
• Each unflagged → check orphaned-from-sector by cross-referencing ticker vs Sector Note's Active Theses. If flag triggers, add to set.
• Unflagged theses passing all checks → excluded from Phase 2 entirely.

Typically reduces full reads from ~40 to 10-20.

Flag additionally during Pass 2:

• High-conviction theses whose Sector Note has been significantly updated but the thesis Log hasn't reflected it

Phase 2: Assess Each Candidate

For each flagged thesis, read full note + supporting research. Assess:

1. Evidence trajectory: strengthening / weakening / going stale since creation?
2. Thesis integrity: does the original non-consensus insight still hold? Has the market moved toward or away?
3. Opportunity cost: is research time here coming at the expense of higher-conviction ideas?
4. Catalyst horizon: specific upcoming event that could reignite?
5. Vault connectivity: well-connected (wikilinks, sector, macro) or isolated bet?

Phase 3: Recommendation

Per candidate, recommend ONE:

⬆️ UPGRADE

• Evidence quietly strengthened; recent research/sector developments support thesis but haven't been reflected in conviction.
• Specify: new conviction level, what justifies it, Log entry to add.

➡️ KEEP MONITORING

• Still valid but needs specific trigger to become actionable.
• Specify: exact trigger (falsifiable + time-bounded), review date (downgrade to CLOSE if trigger hasn't fired).

⬇️ CLOSE

• Evidence weakened, insight absorbed by consensus, no catalyst, or never properly developed.
• Specify: one-line rationale. Offer to move to _Archive/ with final Log entry.
• "Absorbed by consensus" closures require an external check — the analysis subagent runs ≤1 WebSearch per CLOSE candidate for 1–2 recent datapoints (analyst note / news item) showing the market now holds the once-non-consensus view. None found → tag the recommendation [unverified: absorbed-by-consensus claim not externally checked]; the tag MUST carry into the Phase 4 Rationale cell and the Phase 5 approval prompt so the user archives with eyes open. Staleness ≠ wrong: a quiet thesis is not a disproven one — do not close on absorption grounds without the datapoint or the tag.

Phase 4: Portfolio Health Summary

Recommendation Table

⚡ Most urgent: [single highest-priority action — e.g. CLOSE TICKER — reason, or none this run]

Ticker	Company	Status	Conviction	Flag(s)	Recommendation	Model trigger	Rationale
					⬆️/➡️/⬇️	[G-#] / Industry # / Lens § / none	[one line]

Model trigger — the mental-model trigger behind the keep/upgrade/close call, cited by stable ID ([G-10], Semis #2, VLM §2) or none; one short ID per recommendation, binding the mandatory Mental-Models read to the deliverable. CLOSE-on-consensus → usually base-rate/outside-view [G-10] or a Value-Layer-Monopoly kill-criterion; KEEP MONITORING → the trigger keeping the thesis alive.

Portfolio Stats

• Total theses: X
• Active / Draft / Monitoring: X / X / X
• Flagged for review: X
• Recommended closures: X
• Recommended upgrades: X
• Average thesis age (days since last Log): X
• Theses with no catalyst: X

Attention Allocation Insight (§9)

• What % of theses are high-conviction? Appropriate or should more be pruned?
• Sectors with too many thin theses needing consolidation?
• Which 3 theses deserve MORE research time (conviction + evidence strength)?

Phase 5: Execute (WITH USER APPROVAL) — Atomic Batch

Do NOT auto-execute. Present table; wait for user confirmation.

Atomic batch pattern (§1): all safety snapshots created BEFORE any destructive modifications. Five sequential stages — each completes fully before the next begins.

Stage 1: Write Batch Manifest Skeleton (C2 — manifest BEFORE any snapshot/destructive op; §2)

Why manifest-first (C2, invariant #11): if /prune crashes between Stage 1 snapshots and Stage 1.5 manifest (prior order), per-thesis pre-closure snapshots exist on disk with snapshot_trigger: prune but no matching manifest. /clean Step 2d 30-day closure floor requires a matching manifest to detect — without it, snapshots fall through to "standard orphan" and can be deleted via /clean orphans the same day. Writing the manifest FIRST binds any subsequent snapshot to the batch ID; closure-floor protection is unbypassable from that moment.

Generate single batch ID for entire prune run:

HHMMSS=$(date +%H%M%S)
mkdir -p _Archive/Snapshots

prune-YYYY-MM-DD-$HHMMSS = snapshot_batch for ALL snapshots (written in Stage 1.5) and matching batch: field in the manifest.

Pre-resolve affected sector notes (read-only, destructive-safe): for each approved thesis sector:, resolve via .claude/skills/_shared/sector-resolution.md. Dedup. Collect the list of (sector_note_path, match_confidence, log_message) tuples. This resolution is needed for the skeleton's ## Affected Sector Notes section and reused by Stage 1.5 snapshots + Stage 4 edits. match_confidence: none skipped from sector updates (Stage 4) and sector snapshots (Stage 1.5).

Write _Archive/Snapshots/_prune-manifest (prune-YYYY-MM-DD-HHMMSS).md:

---
type: prune-manifest
batch: prune-YYYY-MM-DD-HHMMSS
status: in-progress
date: YYYY-MM-DD
---

Body:

# Prune Batch Manifest

> **If `status: in-progress`**, `/prune` did not complete successfully.
> Recovery: `/rollback [any ticker below]` → select `(pre-prune)` → cascade (a).
> Then delete this manifest and re-run `/prune`.
>
> **If `status: completed`**, prune finished but Stage 5 cleanup didn't. Safe to delete
> manually. `/clean` and `/lint #36` also surface these.

## Intended Closures
- TICKER1 - Company1
- TICKER2 - Company2

## Intended Upgrades
- TICKER3 - Company3 (conviction low → medium)

## Affected Sector Notes
- Sector Name (closures: TICKER1, TICKER2; upgrades: TICKER3)

## Downstream Content Propagation (Stage 4.2 targets)
- Neighbor theses receiving closure-notification Log entries: *(populated at Stage 4.5 after Stage 2 neighbor scans complete — C1)*
- Macro notes referencing closed theses (reported only): *(populated at Stage 4.5 after 4.2a scan)*

Skeleton write failure → hard abort Stage 5 before any snapshot. Report to user; no destructive edits have run yet. /clean's closure-snapshot 30-day floor is trivially unbypassable when there are no snapshots yet.

Flipped to completed then retained at Stage 5 (§3). Body's Downstream Content Propagation section populated at Stage 4.5 with the deduplicated neighbor list (C1 fix — prior spec left placeholders unfilled, breaking /rollback Step 6.2.5 Tier B surfacing).

Stage 1.5: Snapshot ALL Affected Files (C2 — after manifest skeleton lands)

Reuse HHMMSS from Stage 1. All snapshots bound to the already-existing manifest via snapshot_batch: prune-YYYY-MM-DD-HHMMSS — they inherit the 30-day closure-floor protection from Stage 1's manifest even if Stage 1.5 crashes mid-snapshot (invariant #11).

Thesis snapshots — one per approved closure AND per approved upgrade. Issue ALL cp calls in ONE Bash block using background shell jobs + wait (mirrors /compare Phase 5.5a and /rollback Step 4 patterns — a 5-closure batch is 5 sequential cp rounds without this; one round-trip with it):

mkdir -p _Archive/Snapshots
# Per approved closure/upgrade, fire cp in background:
cp "Theses/TICKER1 - Name1.md" "_Archive/Snapshots/TICKER1 - Name1 (pre-prune YYYY-MM-DD-HHMMSS).md" &
cp "Theses/TICKER2 - Name2.md" "_Archive/Snapshots/TICKER2 - Name2 (pre-prune YYYY-MM-DD-HHMMSS).md" &
cp "Theses/TICKER3 - Name3.md" "_Archive/Snapshots/TICKER3 - Name3 (pre-prune YYYY-MM-DD-HHMMSS).md" &
wait
# Check exit status of all background jobs before proceeding to frontmatter Edits

Then issue all frontmatter-addition Edits as a single parallel tool-call batch (one Edit per snapshot, all in the same message):

snapshot_of: "[[Theses/TICKER - Company Name]]"
snapshot_date: YYYY-MM-DD
snapshot_trigger: prune
snapshot_batch: prune-YYYY-MM-DD-HHMMSS

Sector note snapshots — use the (sector_note_path, match_confidence, log_message) tuples resolved in Stage 1. Dedup, then snapshot each unique sector note in the SAME background-jobs Bash block as the thesis snapshots above (one wait for all snapshots across both categories). Frontmatter (snapshot_trigger: prune, same batch ID).

match_confidence: none → skipped from snapshot and from Stage 4 sector update per Stage 1 resolution. normalized/substring → log_message collected for final report.

Abort gate (§1.3): snapshot creation fails → STOP immediately. Report ❌ Snapshot failed for [file]. Prune aborted — no downstream mutations. Fix the issue and re-run /prune. Manifest skeleton persists with status: in-progress; /lint #36 surfaces. User can rm the manifest manually after resolving the failure.

Stage 2: Process ALL Thesis Closures

Neighbor-grep batch (parallel): before iterating closures, issue ALL neighbor greps in ONE parallel tool-call batch — one Grep per closure, all in the same message. Each Grep uses the wikilink patterns below against Theses/ (excluding the thesis being archived). Alternatively (fewer tool calls), issue a single Grep with alternation across all closure filenames:

Grep pattern='\[\[(Theses/)?(TICKER1 - Name1|TICKER2 - Name2|TICKER3 - Name3)(\.md)?(#[^\]|]+)?(\|[^\]]+)?\]\]' path='Theses/' glob='*.md' output_mode='content' -n

For a 5-closure batch this is 1-5 Greps in one round-trip instead of 5 sequential rounds. Partition the combined results per closure (by which filename alternation branch matched each line) in the reasoning layer.

For each approved closure:

1. Append final Log entry: ### YYYY-MM-DD\n- CLOSED: [rationale]. Archived.

2. Change frontmatter: status: closed.

3. Record neighbor list for graph invalidation (from the parallel batch above — no additional Grep per closure). Wikilink patterns covered by the batch:

   • [[Theses/TICKER - Name]], [[Theses/TICKER - Name|...]], [[Theses/TICKER - Name#...]], [[Theses/TICKER - Name.md]]
   • [[TICKER - Name]], [[TICKER - Name|...]], [[TICKER - Name#...]]

   Dedup per closure → that closure's neighbor set.

4. Move file:

   mv "Theses/TICKER - Company Name.md" "_Archive/TICKER - Company Name.md"
   

5. Archive-ticker registry (supports /thesis Signal C): append to .archive_ticker_registry.md at vault root. Create with header on first write:

   REGISTRY=".archive_ticker_registry.md"
   if [ ! -f "$REGISTRY" ]; then
     cat > "$REGISTRY" <<'HEADER'
   ---
   type: archive-ticker-registry
   purpose: Flat append-only log of thesis archival events. Consumed by /thesis Step 1.2 Signal C (multi-signal archive-collision check).
   ---
   
   # Archive Ticker Registry
   
   HEADER
   fi
   printf '%s|%s|%s|%s|%s\n' \
     "$TICKER" "$ARCHIVED_FILENAME" "$(date +%Y-%m-%d)" \
     "$CONVICTION_AT_CLOSURE" "$CLOSURE_RATIONALE_LINE" \
     >> "$REGISTRY"
   

   Registry append failure does not abort — log warning and continue.

Do NOT update sector notes here (batched in Stage 4). Do NOT write .graph_invalidations per-closure (batched in Stage 4.5 — §5.1).

Closure mid-stage failure: report completed/failed/pending. Pre-prune snapshots available. Manifest persists.

⚠️ Closure failed for [TICKER] at step [N]. Completed: [list]. Failed: [list]. Pending: [list].
All pre-prune snapshots available (batch: prune-YYYY-MM-DD-HHMMSS).
Batch manifest: [[_Archive/Snapshots/_prune-manifest (prune-YYYY-MM-DD-HHMMSS)]]
To recover: /rollback [any affected ticker] → select (pre-prune) → cascade (a) to restore all.
Sector notes have NOT been modified — no sector inconsistency from this partial failure.
After recovery, delete the batch manifest.

Session crash (no error): manifest persists with embedded recovery instructions. /lint #36 surfaces.

Stage 3: Process ALL Upgrades

For each approved upgrade:

1. Update conviction: in frontmatter.
2. Append Log entry (max 2 lines):

   ### YYYY-MM-DD
   - Prune upgrade [old] → [new]: [what justified] — conviction strengthened, [reason]
   

   Prefix "Prune upgrade" — /sync Step 2.5 skill-origin classification (registry §9).

Stage 4: Update ALL Sector Notes

Per affected sector note (identified in Stage 1):

1. Read current sector note.
2. Closures: remove archived theses from Active Theses. If ## Closed/Archived section exists, add them there.
3. Upgrades: if sector note displays conviction alongside thesis links, update to reflect new levels.

Do NOT rewrite wikilinks across the vault in this stage. Downstream content propagation (Stage 4.2) is append-only.

Graph update deferred: _graph.md owned exclusively by /graph. Run /graph last after this skill.

Stage 4.2: Propagate Closures to Downstream Content (closures only)

Skip if Stage 2 processed zero closures. Neighbor thesis sets from Stage 2 step 3 reused here (§4.1).

4.2a: Identify downstream files per closure

For each closed thesis, two target groups:

1. Cross-referencing theses: already collected in Stage 2 step 3.
2. Macro notes: grep Macro & Technology/*.md for same wikilink patterns used in Stage 2 step 3.

Exclude _Archive/, _Archive/Snapshots/, _Inbox/processed/, .git/ from both scans.

4.2b: Append closure-notification Log entry to affected theses

Per neighbor thesis from 4.2a step 1, append single dated Log entry:

### YYYY-MM-DD
- Cross-thesis closure: [[_Archive/CLOSED_TICKER - Company Name]] archived — [one-line rationale]. Cross-thesis and Related Research wikilinks retained; review body prose if thesis impact has changed.

Rules (§4.2-§4.5):

• One Log entry per affected thesis regardless of closure count. Multi-closure case: Cross-thesis closures: [[_Archive/TICKER1 - ...]], [[_Archive/TICKER2 - ...]], [[_Archive/TICKER3 - ...]] archived this run — ...
• Max 2 lines per CLAUDE.md Writing Standards. Collapse long lists: ... and 2 more — see /prune output.
• Archive-path wikilinks: [[_Archive/TICKER - Company Name]] (§4.3 — Obsidian resolves natively; no broken-link display).
• Do NOT modify body prose — Log annotation is the notification; user reviews body at their pace.
• Do NOT snapshot for 4.2b — Tier B append-only (§4.2). Append failure → thesis unchanged.

Prefix "Cross-thesis closure:" / "Cross-thesis closures:" — /sync Step 2.5 skill-origin + Step 3e drift exclusion (registry §13).

Append failure → log + continue. Report failures in Stage 5 summary.

4.2c: Macro note handling — detect and report only (§4.4)

Auto-editing narrative prose can destroy analytical coherence. For each macro note from 4.2a step 2:

• Do NOT edit the file.
• Collect (macro note path, affected-thesis list) pairs for Stage 5 report.
• Surface:

  ⚠️ Macro references to closed theses — review manually:
    - [[Macro & Technology/Iran conflict — Transmission Map]] references [[CLOSED_TICKER1 - ...]] (now archived)
    - [[Macro & Technology/AI capex cycle]] references [[CLOSED_TICKER1 - ...]], [[CLOSED_TICKER2 - ...]] (now archived)
  

User decides per macro note: (a) rewrite prose, (b) leave as historical, (c) strikethrough/annotate.

4.2d: Stage report fields

Include in Stage 5 report:

• Cross-thesis Log annotations: [N] neighbor theses received closure-notification entries: [list]. [M] Edit failures: [list with reason].
• Macro notes referencing closures: [N] macro notes contain wikilinks to archived theses — manual review: [list pairs].

Stage 4.5: Write Graph Invalidation List + Populate Manifest Neighbor List (closures only; C1 + §5.1)

Skip if Stage 2 processed zero closures. For closure runs, this stage performs two related writes:

(1) Write .graph_invalidations — merge every closure's neighbor set (from Stage 2 step 3) into one deduplicated list, append to .graph_invalidations:

{
  [ -f .graph_invalidations ] && cat .graph_invalidations
  # Deduplicated union of Stage 2 neighbor sets (all closures):
  printf '%s\n' "Theses/NEIGHBOR1 - ...md" "Theses/NEIGHBOR2 - ...md" ...
} | sort -u > .graph_invalidations.tmp && mv .graph_invalidations.tmp .graph_invalidations

Batched once per prune run — not per-closure.

Write failure → report, do NOT abort (§5.2). Closures/upgrades/sector updates already succeeded. ⚠️ .graph_invalidations write failed — run /graph (full rebuild) instead of /graph last to clean stale cross-thesis refs.

(2) Populate manifest body neighbor list (C1 — makes /rollback Step 6.2.5 Tier B surfacing work): Edit the Phase 1 manifest skeleton, replacing the *(populated at Stage 4.5 ...)* placeholders under ## Downstream Content Propagation with the actual deduplicated values:

## Downstream Content Propagation (Stage 4.2 targets)
- Neighbor theses receiving closure-notification Log entries:
  - [[Theses/NEIGHBOR1 - Company1]] (appended: succeeded | failed reason)
  - [[Theses/NEIGHBOR2 - Company2]] (appended: succeeded)
  - ...
- Macro notes referencing closed theses (reported only, not edited):
  - [[Macro & Technology/Example Macro Note]] — references [[_Archive/CLOSED_TICKER1 - ...]], [[_Archive/CLOSED_TICKER2 - ...]]
  - ...

Sources for the populated list:

• Neighbor theses: union of Stage 2 step 3 per-closure neighbor sets, paired with Stage 4.2b's per-neighbor append outcome (succeeded | failed reason).
• Macro notes: output of Stage 4.2a step 2 grep + 4.2c surface-only report (no edits applied).

Manifest body Edit failure → log warning, continue. The .graph_invalidations write already succeeded; the missing neighbor list only affects /rollback Step 6.2.5's ability to surface Tier B entries automatically — user can fall back to manual grep via the Cross-thesis closure: prefix. /lint #36 will flag the placeholder survival as Nice to Have.

Why this matters: prior spec left the placeholder strings in the manifest body. /rollback Step 6.2.5 reading the manifest would surface literal text *(populated at Stage 4.5 ...)* to the user instead of real ticker names — breaking the documented Tier B review flow. Populating the placeholder closes that gap.

_hot.md update

Per .claude/skills/_shared/hot-md-contract.md (do NOT touch Latest Sync / Sync Archive):

1. Active Research Thread: same-ticker continuation per contract. Write: pruned portfolio — [N] closed, [N] upgraded, [next step].
2. Recent Conviction Changes: per-upgrade and per-closure entries. Never compressed per contract.
3. Open Questions: remove questions related to closed theses. Add new questions raised by upgrades.
4. Portfolio Snapshot: update conviction-level counts + sector coverage if materially changed.

Word cap: after edits, check total. Over 8,000 (soft cap per _shared/hot-md-contract.md) → prune ## Sync Archive (oldest first) then *Previous:* lines. Abort if over 10,000 hard cap.

Stage 5: Manifest Retention (§3 — 30-day regret window)

All stages complete. /prune retains the manifest (§3.2 — changed from prior delete-at-completion behavior):

1. Flip manifest status: Edit frontmatter — status: in-progress → status: completed. Add completed_date: YYYY-MM-DD.

2. Verify flip landed (Edit-return inspection — no re-read): inspect the frontmatter-flip Edit's return value. The Edit tool reports success iff the replacement landed; the returned snippet shows the post-edit frontmatter. Confirm status: completed present, status: in-progress absent from the Edit-return content.

   • Success → manifest stays in _Archive/Snapshots/ with status: completed. /clean + /lint #36 handle aging.
   • Verification failure (§3.4 — Edit-return indicates replacement did not produce expected frontmatter, or Edit tool returned error): do NOT attempt repair. Report:

     ❌ Manifest status flip failed: [[_Archive/Snapshots/_prune-manifest (prune-YYYY-MM-DD-HHMMSS)]] is still marked in-progress despite successful prune completion.
     
     DO NOT run /rollback — the prune closures/upgrades/sector updates/downstream propagation have all succeeded; rolling back would undo valid work.
     
     Manual fix: open the manifest and replace status: in-progress with status: completed. The manifest will then age out via /clean after 30 days. /lint #36 flagging it as Critical is a false alarm in this specific case.
     

     Exit.

3. NO deletion step. Manifest persists until /clean removes it (30 days after completed_date:) or user rms manually.

Retention policy

• Days 0-30 after completed_date:: manifest stays. /rollback cascade can find batch and surface Tier B Log entries for neighbor review during regret-recovery. /lint #36 Pass.
• Days 30+: /clean (any mode) removes via Step 2a extension. /lint #36 Nice to Have.

User regret-recovery flow:

User realizes approved /prune closure was wrong.
If `completed_date:` within 30 days:
  /rollback [any ticker from manifest's Intended Closures]
  → select (pre-prune) snapshot → cascade (a) to restore all files
  → /rollback Step 6.2.5 surfaces neighbor Tier B Log entries for strikethrough review
  → delete manifest manually after recovery: rm "_Archive/Snapshots/_prune-manifest..."

Stage 5 Final Report

• Closures completed: [N] (list with rationales)
• Upgrades completed: [N] (list with old → new)
• Sector notes updated: [list]
• Cross-thesis Log annotations: [N] neighbors received closure-notification entries: [list]. [M] Edit failures: [list with reason].
• Macro notes referencing closures: [N] macros contain wikilinks to archived theses — manual review: [list pairs].
• Graph invalidation: [N] neighbors queued in .graph_invalidations | no neighbors | write failed — recommend /graph (full)
• Manifest state: completed — retained for 30-day regret-recovery window | ⚠️ flip verification failed — do NOT /rollback, resolve manually per warning above
• Graph reminder: → Run /graph last to update the dependency map. (Closure runs require this to clear stale cross-thesis refs.)
• Sector resolution logs (if normalized or substring): list contract's log_message entries.