| name | alive:system-cleanup |
| description | The world feels messy. Stale tasks, orphan folders, v2 remnants, unsaved sessions — entropy is accumulating and needs to be addressed before it compounds. Scans across all walnuts, then surfaces issues one at a time. |
| user-invocable | true |
Tidy
System maintenance. Root health first, then one walnut at a time. Surfaces issues with recommended fixes — the human picks.
Not a dashboard (that's world). Not a search (that's find). Not session history (that's alive:session-history). Pure maintenance.
v3 Architecture Reference
Walnut structure is flat under _kernel/:
walnut-name/
_kernel/
key.md
log.md
insights.md
tasks.json
now.json
completed.json
bundle-a/
context.manifest.yaml
raw/
bundle-b/
context.manifest.yaml
There is NO _kernel/_generated/ subdirectory. There is NO bundles/ container directory. Bundles sit as direct children of the walnut root alongside _kernel/.
Task operations go through tasks.py, never by reading/writing task files directly:
tasks.py list --walnut {path} — all active tasks as JSONtasks.py list --walnut {path} --status active — filter by statustasks.py summary --walnut {path} — structured summary with counts
Projection rebuilds go through project.py:
project.py --walnut {path} — rebuilds _kernel/now.json
Three-Phase Flow
Phase 1: Root Audit (system-level, 7 checks — parallel subagents)
|
Phase 2: Walnut Summary (single subagent scans frontmatter, human picks)
|
Phase 3: Deep Audit (one walnut, 12 checks — parallel subagents)
Subagent Strategy (non-negotiable)
Tidy is read-heavy. Every phase uses subagents to keep the main context clean.
Discovery subagents MUST use subagent_type: "Explore" — Explore agents have direct file read access without needing Bash. Use Explore for all Phase 1, Phase 2, and Phase 3 discovery checks.
Fix-execution subagents MUST use subagent_type: "general-purpose" — only general-purpose agents have Write/Edit access. Dispatch one general-purpose agent per approved fix.
- Phase 1: Dispatch all 7 root checks as parallel subagents. Wait for all. Present results together — one line per passing check, expand on failures only.
- Phase 2: Single subagent reads all walnut frontmatter, returns the health table.
- Phase 3: Dispatch all 12 checks as parallel subagents (one check per subagent). Wait for all. Present results together — passing checks collapsed, failures expanded one at a time.
Each subagent gets: the subagent brief (read $ALIVE_PLUGIN_ROOT/templates/subagent-brief.md once, prepend to every agent prompt), the check description, what to scan, what constitutes a pass/fail, and instructions to return a structured result (pass/fail + details if fail). Without the brief, subagents will not understand walnut/bundle structure, tasks.py, or v3 conventions.
Never read walnut files in the main context. All file reading happens inside subagents. The main context only sees results.
Presentation Rules
- Passing checks: Collapse to one line.
✓ 3a. now.json zero-context — pass. No details.
- Failing checks: Expand with bordered block, recommended fix, and options. One at a time.
- After presenting all results: Walk through failures one at a time for the human to resolve or skip.
Phase 1 — Root Audit
Dispatch 7 subagents in parallel. Each checks one thing across the whole world.
1a. ALIVE Structure
Verify all 5 ALIVE folders exist at the world root (01_Archive/ through 05_Experiments/).
Pass: all 5 exist. Fail: any missing.
1b. Inputs Buffer
Scan 03_Inbox/ for items older than 48 hours. Unrouted inputs may contain decisions or context affecting active walnuts.
Pass: empty or nothing older than 48h. Fail: items found.
╭─ 🐿️ tidy — unrouted inputs
│ 03_Inbox/ has 3 items older than 48 hours:
│ - vendor-brochure.pdf (3 days)
│ - meeting-notes-feb20.md (4 days)
│
│ ▸ route via alive:capture-context / skip
╰─
1c. Cross-Walnut Links
Scan ALL walnuts' _kernel/key.md frontmatter (links: and parent: fields) AND body text for [[wikilinks]]. Check for:
- Broken wikilinks — links pointing to walnut names that don't exist as folders
- Orphan parents —
parent: pointing to a non-existent walnut
- Undeclared connections —
[[wikilinks]] used in body text or log entries but NOT in the frontmatter links: field. These are invisible to alive:search-world traversal.
- Structureless folders — folders in ALIVE domains (02-05) that have no
_kernel/ but look like they should be walnuts
1d. Walnut Structural Integrity
Quick scan that every walnut has the full v3 flat _kernel/ skeleton:
- 3 narrative files:
_kernel/key.md, _kernel/log.md, _kernel/insights.md
- 2 data files:
_kernel/tasks.json, _kernel/now.json
- 1 archive file:
_kernel/completed.json
There is NO _kernel/_generated/ subdirectory expected. There is NO bundles/ container directory expected. If either is found, that is a separate check (see 1d does not flag these — checks 3k and 3l handle v2 remnant detection during deep audit).
Pass: all walnuts have all 6 files in flat _kernel/. Fail: list what's missing where.
1e. Unsaved Squirrel Entries
Scan .alive/_squirrels/ (world-level) for YAML files where saves: 0 (never saved). Flag entries that have stash items — those contain unrouted decisions/tasks. For entries with saves: 0 and empty stash, check transcript file size to distinguish "opened and closed" from "real work, never saved."
Separate entries with stash (need review) from empty shells (safe to clear).
╭─ 🐿️ tidy — unsaved sessions
│ 3 sessions with unrouted stash:
│ - stellarforge / squirrel:67b1e464 — 4 stash items
│ - glass-cathedral / squirrel:45dcf404 — 6 stash items
│ 13 empty shells (no walnut, no stash) — safe to clear.
│
│ ▸ review stellarforge stash / review glass-cathedral stash / clear empty shells / skip
╰─
1f. Orphan Files at World Root
Flag anything at the world root that isn't an ALIVE folder (01_Archive/ through 05_Experiments/), .alive/, .claude/, or dotfiles. Nothing should live loose at root.
1g. Index Staleness
Check if .alive/_index.yaml exists and when it was last generated. If it doesn't exist or is older than 7 days, offer to regenerate by running generate-index.py.
Pass: index exists and is recent. Fail: missing or stale — offer to regenerate.
Phase 1 Results
Present all 7 results together. Passing checks get one line. Failures expand.
╭─ 🐿️ root audit — 7 checks
│
│ ✓ 1a. ALIVE structure — intact
│ ✓ 1b. Inputs buffer — clean
│ ⚠ 1c. Cross-walnut links — 2 undeclared connections
│ ✓ 1d. Walnut integrity — all complete
│ ⚠ 1e. Unsaved entries — 3 with stash, 13 empty
│ ⚠ 1f. Orphan files — 2 at root
│ ✓ 1g. Index — current
│
│ 3 issues to resolve.
╰─
Then ask which to fix:
╭─ 🐿️ root audit — which to fix?
│
│ 1. 2 undeclared cross-walnut connections
│ 2. 3 unsaved sessions with stash (11 items total)
│ 3. 2 orphan files at world root
│
│ ▸ which ones? (numbers, "all", or "skip")
╰─
For each the human picks, propose the specific fix:
╭─ 🐿️ proposed fixes
│
│ 1. Add [[ryn-okata]], [[jax-stellara]] to stellarforge key.md links:
│ 3. Move AGENTS.md → glass-cathedral/raw/,
│ delete disaster-recovery-extraction.md
│
│ ▸ go / change something / skip
╰─
On "go": dispatch parallel general-purpose subagents to execute — one per fix. Each subagent reads the file, makes the edit, returns confirmation. Main context does not touch files.
╭─ 🐿️ root audit complete
│ 7 checks. 3 issues, 2 fixed, 1 skipped.
│ ▸ continue to walnut audit / done
╰─
Phase 2 — Walnut Summary
Single subagent scans all walnuts. For each walnut, read ONLY _kernel/now.json (v3 flat path) and _kernel/key.md frontmatter (rhythm, type). Frontmatter only. Do not read full files.
Return a health table. The main context presents it:
╭─ 🐿️ walnut health summary
│
│ # Walnut Type Health Updated Rhythm
│ 1. glass-cathedral experiment active 2 hours ago weekly
│ 2. stellarforge venture active 2 days ago weekly
│ 3. nova-station venture quiet 12 days ago weekly ⚠
│ 4. glass-cathedral experiment waiting 34 days ago monthly ⚠
│
│ Which walnut to audit? (number, or "done" to finish)
╰─
Health thresholds (from rhythm):
| Rhythm | Quiet at | Waiting at |
|---|
| daily | 2 days | 4+ days |
| weekly | 2 weeks | 4+ weeks |
| fortnightly | 3 weeks | 6+ weeks |
| monthly | 6 weeks | 3+ months |
Post-migration note: If many walnuts show today's date with "active" health, the data may reflect migration timestamps rather than genuine recent work. Flag this to the human if detected (e.g., 5+ walnuts all updated on the same day).
Phase 3 — Deep Audit (single walnut)
Dispatch 12 subagents in parallel — one per check. Each subagent reads only the files it needs from the walnut's _kernel/ and its bundle directories. Do not read the brief pack in the main context.
The main context receives pass/fail results from all 12 subagents, presents them together, then walks through failures one at a time.
3a. Malformed Files (runs first conceptually — other checks depend on frontmatter)
Scan ALL .md files in _kernel/ and in bundle directories (directories at the walnut root that contain context.manifest.yaml). Check each .md file starts with --- followed by valid YAML and a closing ---.
Pass: all files have frontmatter. Fail: list files without it.
Fix guidance: When the human picks "add frontmatter now", read the file body to determine:
- System file → use the schema from conventions (type-specific required fields)
- Bundle manifest → add: type, description, date, squirrel, tags + type-specific fields
3b. Walnut Skeleton
Check that all 6 v3 kernel files exist in the flat _kernel/ directory:
_kernel/key.md_kernel/log.md_kernel/insights.md_kernel/tasks.json_kernel/now.json_kernel/completed.json
Pass: all present. Fail: list what's missing.
If _kernel/now.json is missing, suggest running project.py --walnut {path} to generate it.
3c. key.md Completeness
Read _kernel/key.md frontmatter and body. Check:
- Required frontmatter fields filled:
type, goal, created, rhythm, tags
people: populated (especially for ventures — empty people on a venture with collaborators is a gap)links: matches body references — if body text uses [[wikilinks]] not declared in links:, flag themtags: not empty
Pass: all fields filled, links match body. Fail: list gaps.
3d. now.json Zero-Context
Read _kernel/now.json (v3 flat path) and _kernel/log.md (frontmatter + first ~100 lines). Apply the zero-context test: "If a brand new agent loaded this walnut with no prior context, would it have everything it needs to continue the work?"
Fail conditions:
- Context paragraph is empty or just a template comment
- Context is one sentence when log shows 3+ recent sessions of substantial work
- Context references things not in the log (hallucinated or outdated)
updated: timestamp is more than 2 weeks old
Fix guidance: When the human picks "rewrite now", suggest running project.py --walnut {path} to regenerate now.json from current sources. If the log itself is stale, note that project.py will produce a stale projection and suggest a manual log entry first.
3e. Urgent task validation
Use tasks.py list --walnut {path} --priority urgent to get urgent tasks. Check:
- At least one urgent or active task exists, OR the walnut is in a phase that doesn't need open work (e.g.
paused, archived, published).
- No urgent task has been sitting untouched longer than the walnut's rhythm window (flag stale urgent items).
Pass: there is a credible top-of-mind action, or the walnut is legitimately at rest. Fail: nothing urgent, nothing active, and the walnut is not paused or archived.
3f. Log Health
Read _kernel/log.md frontmatter and first ~150 lines. Check:
- Entries are prepend-ordered (newest at top, dates descending)
- Recent entries are signed (
signed: squirrel:[session_id])
entry-count: in frontmatter is roughly accurate (within +/-5 of actual)last-entry: in frontmatter matches the top entry's date
Pass: ordered, signed, counts match. Fail: list specific issues.
3g. Stale Walnut Past Rhythm
Compare _kernel/key.md rhythm against _kernel/now.json updated timestamp using the Phase 2 thresholds.
Pass: within rhythm. Fail: quiet or waiting.
╭─ 🐿️ tidy — stale walnut
│ nova-station has been quiet for 18 days (rhythm: weekly)
│ Last entry: Feb 5 — "locked episode 11 structure"
│
│ ▸ open it / archive it / change rhythm / skip
╰─
3h. Bundles and Manifests
Scan bundle directories (direct children of walnut root that contain context.manifest.yaml). Check:
- Orphan raw files — files in
raw/ subdirectories with no corresponding context.manifest.yaml in the parent bundle
- Manifest schema — manifests that exist but are missing required fields (
type:, description:, date:). A manifest without description: is almost as invisible as no manifest.
Pass: all raw files have manifests, all manifests have required fields. Fail: list gaps.
3i. Stale Bundle Drafts
Check bundle directories for bundles with status: draft in their context.manifest.yaml that are older than 30 days (by date: field or file modification time).
Pass: nothing older than 30 days in draft. Fail: list stale bundles.
╭─ 🐿️ tidy — stale draft
│ submission-draft/ — 39 days in draft status
│ ▸ promote to prototype / archive / delete / skip
╰─
3j. Completed Bundles Needing Cleanup
Scan bundle directories for bundles whose context.manifest.yaml has status: done or status: published. These bundles have completed their lifecycle and may contain working files, draft iterations, or temporary artefacts that can be cleaned up or archived.
Check each done/published bundle for:
- Temporary or working files (e.g.,
*-draft-*.md, *.tmp, *.bak)
- Multiple version files where only the final matters (e.g.,
proposal-v1.md, proposal-v2.md alongside proposal-v3.md)
- Large raw files that could be archived
Pass: no cleanup candidates found. Fail: list bundles with cleanup opportunities.
╭─ 🐿️ tidy — completed bundle cleanup
│ shielding-review/ (status: published) has 3 draft iterations
│ ▸ archive drafts / delete drafts / skip
╰─
3k. v2 Remnant Detection
Check for v2 architecture remnants that need migration:
bundles/ container directory — In v3, bundles sit as direct children of the walnut root. A bundles/ directory at the walnut root is a v2 remnant. Suggest moving its contents up one level._kernel/_generated/ subdirectory — In v3, now.json lives directly in _kernel/. A _generated/ subdirectory inside _kernel/ is a v2 remnant. Suggest moving now.json up and removing the directory.tasks.md without tasks.json — Scan the walnut recursively for tasks.md files. If a tasks.md exists in a directory that has no corresponding tasks.json, flag it as a v2 remnant needing migration. The tasks.md format is no longer read by tasks.py.
Pass: no v2 remnants found. Fail: list each remnant with migration instruction.
╭─ 🐿️ tidy — v2 remnants
│ bundles/ container directory found — 4 bundles inside
│ _kernel/_generated/ directory found — contains now.json
│ 2 tasks.md files found without tasks.json counterpart
│
│ ▸ migrate all / review individually / skip
╰─
Migration instructions per remnant type:
bundles/ — move each child directory up to walnut root, then remove empty bundles/_kernel/_generated/ — move now.json to _kernel/now.json, then remove _generated/tasks.md without tasks.json — parse tasks.md and create corresponding tasks.json using tasks.py add
3l. Orphan Folder Detection
Scan all direct child directories of the walnut root. Flag any directory that:
- Is NOT
_kernel/
- Is NOT
raw/
- Does NOT contain a
context.manifest.yaml
These are orphan folders — they exist in the walnut but have no manifest, so they are invisible to the context system. They may be leftover working directories, unmigrated content, or directories that need a manifest added.
Pass: all non-system child directories have manifests. Fail: list orphan folders.
╭─ 🐿️ tidy — orphan folders
│ 3 folders with no context.manifest.yaml:
│ - scratch-notes/
│ - old-research/
│ - meeting-prep/
│
│ ▸ add manifests / archive / delete / skip
╰─
3m. Stale Tasks via tasks.py
Use tasks.py list --walnut {path} --status active to get all active tasks as structured JSON. Each task includes a created date field.
Stale task detection: Filter tasks where created date is more than 14 days ago and status is still active or todo. These tasks may be stuck, forgotten, or no longer relevant.
Also check:
- Tasks with
status: blocked that have no recent log entries mentioning them
- Tasks with a
due date that has passed
╭─ 🐿️ tidy — stale tasks
│ 3 tasks older than 14 days with no progress:
│ - t012: "Send post-launch message to Ryn" (created 2026-03-10)
│ - t015: "Review shielding spec" (created 2026-03-05, due: 2026-03-20 — OVERDUE)
│ - t018: "Update API docs" (created 2026-03-01)
│
│ ▸ still relevant / remove / reprioritise / blocked (note why) / skip
╰─
Phase 3 Results
Present all 12 results together. Passing checks collapsed, failures listed.
╭─ 🐿️ stellarforge audit — 12 checks
│
│ ✓ 3a. malformed files — all 34 .md files have frontmatter
│ ✓ 3b. walnut skeleton — complete (6/6 kernel files)
│ ⚠ 3c. key.md completeness — links: [] but body references 4 people
│ ✓ 3d. now.json zero-context — pass
│ ✓ 3e. urgent task — top urgent task fresh, aligns with phase
│ ✓ 3f. log health — ordered, signed, counts match
│ ✓ 3g. stale rhythm — active
│ ✓ 3h. bundles — all manifests valid
│ ✓ 3i. stale drafts — none
│ ✓ 3j. completed bundles — clean
│ ⚠ 3k. v2 remnants — bundles/ container found, 1 tasks.md without tasks.json
│ ⚠ 3l. orphan folders — 2 folders without manifests
│ ⚠ 3m. stale tasks — 3 tasks older than 14 days
│
│ 4 issues to resolve.
╰─
Ask which to fix:
╭─ 🐿️ stellarforge — which to fix?
│
│ 1. key.md links: [] but body references 4 person walnuts
│ 2. bundles/ container + 1 tasks.md needing migration
│ 3. 2 orphan folders without manifests
│ 4. 3 stale tasks older than 14 days
│
│ ▸ which ones? (numbers, "all", or "skip")
╰─
For each the human picks, propose the specific fix:
╭─ 🐿️ proposed fixes
│
│ 1. Add [[ryn-okata]], [[jax-stellara]], [[mira-solaris]],
│ [[orion-vex]] to stellarforge `_kernel/key.md` frontmatter links: field
│ 2. Move 4 bundle directories from bundles/ to walnut root,
│ migrate tasks.md in submission-draft/ to tasks.json
│ 3. Add context.manifest.yaml to scratch-notes/ and old-research/
│
│ ▸ go / change something / skip
╰─
On "go": dispatch parallel general-purpose subagents to execute — one per fix. Each subagent reads the file, makes the edit, returns confirmation. Main context does not touch files.
╭─ 🐿️ stellarforge — fixes applied
│
│ ✓ `_kernel/key.md` links updated — 4 person walnuts added
│ ✓ bundles/ migrated — 4 directories moved, tasks.md converted
│ ✓ manifests added — 2 orphan folders now have context.manifest.yaml
│ ✗ stale tasks — skipped
│
│ ▸ audit another walnut / done
╰─
If "audit another walnut" — return to Phase 2 summary with updated health flags.
If "done" — Final Summary.
Final Summary
╭─ 🐿️ tidy complete
│
│ Root: 7 checks, 3 issues, 2 resolved
│ stellarforge: 12 checks, 4 issues, 3 resolved
│
│ 9 resolved, 2 skipped. World is healthy.
╰─
After presenting the final summary, write the current date to .alive/.last_tidy so the session hook can track when tidy was last run:
date -u +"%Y-%m-%d" > "$WORLD_ROOT/.alive/.last_tidy"
