Memory Cleanup

Memory Cleanup — Manual Dream Process

Implements the 4-phase memory consolidation process modelled after Claude Code's Auto Dream feature. Run after major refactors, framework migrations, or every 5+ sessions in a repo.

The memory system lives at ~/.claude/projects/<encoded-cwd>/memory/ and consists of:

• MEMORY.md — index file (must stay under 200 lines; lines after 200 are truncated by the harness).
• Topic files — one Markdown file per memory entry with YAML frontmatter (name, description, metadata.type).

The four memory types are user, feedback, project, reference (see global auto memory instructions for semantics). This skill never invents new types.

Argument Handling (Phase 0)

This skill accepts two optional flags. Default (no flag) runs the interactive 4-phase consolidation defined below.

Flags are mutually exclusive — passing both is an error. Absence of both = legacy interactive mode (Phases 1-4 below).

--dry-run flow:

• Read MEMORY.md and topic files (read-only).
• Produce the same internal plan the interactive mode would (merges, prunes, rewrites).
• Serialisation contract (#717 — load-bearing, read before writing the proposal): applyPendingDream() in scripts/lib/auto-dream.mjs consumes ONLY the FIRST fenced code block in the sidecar body and writes it VERBATIM as the complete new MEMORY.md. It does NOT parse or apply git-style diff hunks. Therefore the proposal MUST ALWAYS be the complete new MEMORY.md body, in EXACTLY ONE fenced ```markdown block — never git-style unified-diff hunks (--- /+++ /@@ … @@ lines), and never multiple fences for MEMORY.md itself. Any topic-file (non-MEMORY.md) change needed by the plan CANNOT be carried inside that single fence — instead, append it AFTER the fence as a separate, clearly-delimited machine-readable section per topic file, using the heading ### Topic-file change: <path> followed by plain-language instruction text (not a diff). These sections are for a human to apply by hand; applyPendingDream() never reads past the first fence. If a ### Topic-file change: section needs to show illustrative code, use 4-space-indented code text, never a fenced ``` block — countFencedBlocks() counts every fence in the raw sidecar body (not just MEMORY.md's), so a second fence anywhere in the document trips the >1-fence unsupported-format guard and blocks the whole apply.
• Call writePendingDream({ repoRoot, diff, sourceSession, memoryLinesBefore, proposedLinesAfter }) from scripts/lib/auto-dream.mjs, passing the single-fence MEMORY.md body (plus any ### Topic-file change: sections) as diff.
• Print one-line status: pending-dream written: <N> lines proposed (or no consolidation needed (MEMORY.md is healthy) when the plan is empty).
• Exit 0 in both branches.

--apply-pending flow:

• Call applyPendingDream({ repoRoot, memoryDir }) from scripts/lib/auto-dream.mjs.
• Behavior matrix on the helper return:
  • applied: true → print auto-dream applied: -<linesBefore-linesAfter> lines, +<entries> consolidated entries and exit 0.
  • applied: false, reason: 'missing' → print no pending dream to apply and exit 1.
  • applied: false, reason: 'stale' → print pending dream is stale (>14d), re-run --dry-run and exit 1.
  • applied: false, reason: 'stale-index' (#788) → print MEMORY.md changed since the producing --dry-run; re-run --dry-run. and exit 1. The sidecar is preserved and MEMORY.md is left untouched (MEMORY.md's mtime is newer than the sidecar's generated_at, so applying the frozen dry-run snapshot would clobber the interim edits).
  • applied: false, reason: 'unsupported-format' → print auto-dream NOT applied: pending-dream.md contains git-style diff hunks this applier cannot consume. MEMORY.md left untouched, sidecar preserved. Re-run /memory-cleanup --dry-run to regenerate a complete-body proposal. and exit 1.
• The sidecar file is deleted on successful apply; staleness (stale / stale-index), missing sidecar, or unsupported-format never deletes anything.

Both flag-driven flows delegate atomicity and staleness enforcement to scripts/lib/auto-dream.mjs. The interactive Phases 1-4 below remain unchanged.

Phase 1: Orient

Understand the current memory state before making changes.

1. List all files in the memory directory:

   ls -la ~/.claude/projects/*/memory/ 2>/dev/null | grep "$(basename "$(pwd)")"
   

   Or directly list the project's memory dir (the path is in the auto memory system instructions).

2. Read MEMORY.md (the index file) — note its line count:

   wc -l <memory-dir>/MEMORY.md
   

3. Skim each topic file referenced in the index. Build a mental map:

   • Which topics are covered?
   • Are there overlapping files?
   • Any files not referenced in the index?
   • Any index entries pointing to files that no longer exist?

Goal: Improve existing files, never create duplicates.

Phase 2: Gather Signal

Find what's changed since the last consolidation.

1. Git history — recent commits give the timeline for "did this fact change?":

   git log --oneline -20
   

2. Stale references — for each file/function/symbol mentioned in memory, verify it still exists:

   grep -rn "specific-file-or-function" src/ lib/ scripts/ 2>/dev/null
   

3. Relative dates — find temporal references that need conversion:

   grep -rni "yesterday\|today\|tomorrow\|last week\|this week\|gestern\|heute\|morgen\|letzte woche" <memory-dir>/
   

4. Version drift — package versions stored in memory vs reality:

   cat package.json | grep '"version"'
   

5. Test/issue-count drift — claims like "5001 passed" or "8 open issues" age fast. Cross-check with current state if mentioned.

Phase 3: Consolidate

Apply maintenance operations to memory files.

3a: Merge overlapping entries

If multiple files or entries describe the same thing, combine them into one authoritative entry. Update inbound [[wiki-link]]s accordingly.

3b: Convert relative dates to absolute

"Yesterday we decided X" → "On 2026-03-24 we decided X". Always use ISO date format (YYYY-MM-DD). This rule applies on write, but cleanup catches what slipped through.

3c: Remove stale references

• Delete entries about files that were removed during refactors.
• Remove debugging notes for bugs that are fixed.
• Update function/file paths that were renamed (git log --diff-filter=R surfaces renames).

3d: Update outdated facts

• Package versions that have been bumped.
• Test counts, issue counts, line counts that changed.
• Feature flags that were toggled.
• Architecture decisions that were reversed (keep a decisions.md-style note that the decision was reversed, with the reason — don't silently overwrite).

3e: Resolve contradictions

If two memory entries conflict, check the codebase to determine which is current. Delete the outdated entry. Never leave contradictions.

Phase 4: Prune & Index

Keep MEMORY.md clean and under the 200-line limit.

1. Check line count:

   wc -l <memory-dir>/MEMORY.md
   

2. If over 180 lines, extract detailed content into topic files. Suggested naming:

   • Session summaries → project_sessions.md or session-YYYY-MM-DD-<slug>.md
   • Architecture decisions → reference_decisions.md
   • Package/tooling details → reference_packages.md
   • Use the convention: {type}_{topic}.md

3. Topic file frontmatter (required):

   ---
   name: descriptive-name
   description: one-line description for relevance matching
   metadata:
     type: project   # one of: user | feedback | project | reference
   ---
   

4. Update the index:

   • MEMORY.md is an index, not a dump.
   • One-line - [Title](file.md) — hook entries.
   • Remove stale pointers to deleted files.
   • Add links for new topic files.
   • Reorder by relevance (most-accessed topics first).

5. Final verification:

   wc -l <memory-dir>/MEMORY.md  # must be < 200
   # verify all index links resolve to existing files
   grep -oP '\]\(([^)]+\.md)\)' <memory-dir>/MEMORY.md | sed 's/](\(.*\))/\1/' | while read f; do
     [ -f "<memory-dir>/$f" ] || echo "BROKEN: $f"
   done
   

Phase 4.5: Worktree-Stale-Sweep (#575 P3.2)

Skip if persistence: false in Session Config. Silent no-op if no Auto-promoted sibling worktrees exist or none are stale.

Detect stale Auto-promoted worktrees (older than stale-branch-days from Session Config, default 7 days) and offer them for batch-removal alongside the other housekeeping prune actions from Phase 4. This sub-phase is additive — it appends candidates to the existing prune flow rather than introducing a separate independent confirmation cycle.

Detection: list candidate auto-promoted worktrees

Auto-promoted worktrees follow the layout <parentDir>/<repoName>-<sessionId>/, where <sessionId> is a semantic session-id (per parseSessionId() from scripts/lib/session-id.mjs). Random-suffix worktrees (UUID-format) are NOT auto-promoted and MUST be ignored.

Authoritative impl: scripts/lib/memory-cleanup/worktree-sweep.mjs — listAutoPromotedWorktrees(repoRoot, mainCheckoutRoot, opts). Import and call; do NOT re-implement from this doc.

Algorithm: split git worktree list --porcelain on the blank-line delimiter; for each worktree entry, skip the main checkout, then require the basename to start with <repoName>- and the suffix to parse as a semantic session-id via parseSessionId() (UUID / random suffixes excluded). Each match yields { wtPath, sessionId, branch }. Any git failure → [] (conservative no-op). Git invocation is via the injection-safe opts.execFileFn (default execFileSync with an args array — #577 HARDEN-001).

Staleness check

A worktree is stale iff mtime(worktree-dir) < now - stale-branch-days × 86400 × 1000. Read stale-branch-days from Session Config (default 7):

Authoritative impl: scripts/lib/memory-cleanup/worktree-sweep.mjs — isWorktreeStale(wtPath, staleBranchDays). Import and call; do NOT re-implement from this doc.

Algorithm: statSync(wtPath); stale iff Date.now() - stat.mtimeMs > staleBranchDays × 24 × 60 × 60 × 1000. A missing or unreadable path → false (conservative no-op).

Integration with the existing housekeeping prune AUQ

After Phase 4 (Prune & Index) compiles its list of items to offer for removal, ALSO include any stale auto-promoted worktrees. The user sees them in the same AUQ ("batch-decide" per PRD §3 P3 Gherkin row 4):

import { execFileSync } from 'node:child_process';
import { listAutoPromotedWorktrees, isWorktreeStale } from '$PLUGIN_ROOT/scripts/lib/memory-cleanup/worktree-sweep.mjs';
import { discoverActiveSessions } from '$PLUGIN_ROOT/scripts/lib/session-discovery.mjs';

const staleBranchDays = $CONFIG['stale-branch-days'] ?? 7;
const candidates = listAutoPromotedWorktrees(process.cwd(), mainCheckoutRoot);
const stale = candidates.filter((c) => isWorktreeStale(c.wtPath, staleBranchDays));

if (stale.length === 0) {
  // Silent no-op — no stale worktrees to offer.
} else {
  // #580-HARDEN-002: cross-check candidates against LIVE peer sessions before offering removal.
  // A stale-by-mtime worktree may still be the checkout of an active parallel session — removing
  // it would disrupt that session (PSA-002 overlap). Flag any such candidate so the AUQ can warn.
  const active = await discoverActiveSessions(mainCheckoutRoot);
  const livePaths = new Set(active.map((s) => s.worktreePath));
  const annotated = stale.map((wt) => ({ ...wt, activePeer: livePaths.has(wt.wtPath) }));

  // Add to the existing housekeeping prune AUQ. Each stale worktree becomes one option line:
  // Format: `[ ] Stale auto-promoted worktree: <basename> (age <N>d) — remove via 'git worktree remove --force'`
  // If `activePeer` is true, prefix the option with "⚠ ACTIVE PEER SESSION" and make Behalten the default.
  //
  // If memory-cleanup currently presents per-item AUQs (one question per prune candidate),
  // append one question per stale worktree.
  //
  // If memory-cleanup uses a single multiSelect AUQ for the whole batch,
  // add stale worktrees as additional options.
  //
  // Operator selects which to remove; coordinator runs (arg-array, no shell — #577 HARDEN-001):
  //   execFileSync('git', ['-C', mainCheckoutRoot, 'worktree', 'remove', '--force', wtPath])
  // for each selected. WARN line per removal.
}

AUQ example (per-item)

When the candidate's wtPath matches a LIVE peer session (wt.activePeer === true, from discoverActiveSessions() above), the AUQ MUST surface a ⚠ ACTIVE PEER SESSION warning and keep Behalten as the safe default — removing a live session's worktree mid-flight is a PSA-002 overlap that can corrupt another session's working state.

const peerWarning = wt.activePeer
  ? ' ⚠ ACTIVE PEER SESSION — removing may disrupt a live session.'
  : '';

AskUserQuestion({
  questions: [{
    question: `Stale auto-promoted worktree found: ${path.basename(wt.wtPath)} (age ${ageDays}d, branch=${wt.branch}).${peerWarning} Remove?`,
    header: "Stale-Worktree",
    multiSelect: false,
    options: [
      {
        label: "Behalten (Recommended)",
        description: wt.activePeer
          ? "Keep this worktree — a LIVE peer session is using it. Removal would disrupt the active session."
          : "Keep this worktree. Re-evaluate at next /memory-cleanup run.",
      },
      {
        label: "Entfernen",
        description: wt.activePeer
          ? `⚠ ACTIVE PEER SESSION detected. Only choose this if you have confirmed no live session needs it, then run 'git worktree remove --force ${wt.wtPath}'.`
          : `Run 'git worktree remove --force ${wt.wtPath}'.`,
      },
    ],
  }],
});

PSA-003 compliance

Per .claude/rules/parallel-sessions.md PSA-003: every git worktree remove is destructive — operator must explicitly authorize. The AUQ above satisfies this. Never auto-remove without user confirmation, even for stale worktrees. The --force flag is acceptable here only because the AUQ already secured explicit per-worktree consent; never apply --force to worktrees the operator did not select.

Cross-references

• PRD: "Parallel-Aware Sessions" (#568; archived in the private Meta-Vault) §3 P3 Gherkin row 4 + §3.A P3 EARS state-driven clause
• stale-branch-days config: scripts/lib/config.mjs:138 (default: 7)
• Detection helper: parseSessionId() from scripts/lib/session-id.mjs
• Stale-sweep helpers: listAutoPromotedWorktrees() + isWorktreeStale() from scripts/lib/memory-cleanup/worktree-sweep.mjs
• Live-peer detection (#580-HARDEN-002): discoverActiveSessions(repoRoot) from scripts/lib/session-discovery.mjs — flags stale candidates whose wtPath matches an active session so the AUQ warns before removal
• PSA-003: .claude/rules/parallel-sessions.md

Output

After completing all four phases, report:

• Files created / updated / deleted (paths only — no full diffs in the chat output).
• MEMORY.md line count (before → after).
• Contradictions resolved (with one-line summary each).
• Stale entries pruned (count + categories).
• Any issues that need manual attention (e.g. ambiguous facts that need user input — surface via AskUserQuestion rather than guessing).

Session-End Signal: "cleanup ran this session" (#699)

A completed cleanup — including a healthy no-op where MEMORY.md was already healthy and no files were mutated — counts as a cleanup run. The session-end skill MUST stamp memory_cleanup_at on the session record whenever /memory-cleanup ran in THIS session, regardless of outcome (dry-run, apply-pending, or no-op).

This advances the auto-dream cadence marker (readDreamSignals → lastCleanupAt in scripts/lib/auto-dream.mjs) so shouldDispatchAutoDream does not fire a false nudge on the next session.

Signalling contract (coordinator responsibility at session-end Phase 3.7):

• Set ranMemoryCleanupThisSession = true when /memory-cleanup ran this session in ANY mode or with ANY outcome.
• Pass this flag to stampMemoryCleanup() from scripts/lib/memory-cleanup-stamp.mjs before emitting the session record (see skills/session-end/session-metrics-write.md § 1-pre).
• Do NOT distinguish between "applied changes" and "healthy no-op" — both count.
• Do NOT set memory_cleanup_at to null; simply omit the field when cleanup did not run.

Anti-Patterns

• Don't rewrite memory you don't understand. If a fact's provenance is unclear, leave it and flag it in the output instead of deleting.
• Don't bulk-delete on the first run. Cleanup runs are cheap; aggressive pruning costs context that can't easily be reconstructed.
• Don't create new memory types. The four-type taxonomy (user, feedback, project, reference) is load-bearing for the relevance heuristic.
• Don't touch MEMORY.md if line-count is already healthy. Re-ordering for its own sake creates churn without value.

Source: hashgraph-online/awesome-codex-plugins → plugins/Kanevry/session-orchestrator/skills/memory-cleanup/SKILL.md