Vault Optimizer

Apply 10 frameworks to every markdown file in the vault. For each framework, read its pass-implementation file, run every check, log findings, walk the user through fixes per item, apply (or save to a plan). Save one comprehensive HTML report grouped by framework. Do not inline the HTML in chat — only the saved path and a one-paragraph summary.

Operating philosophy — read carefully, this is what makes this skill different

1. Every finding ships a concrete fix. No flag-only. No "warn and forget." No manual-review pile. When the user runs apply-mode, every finding becomes either an applied edit, a saved migration step in a dated reorg plan, or (only if the user explicitly declines this finding in walk) a recorded decline. Nothing lingers as an open warning across runs.
2. Severity is informational, not gating. fail / warn / info describes how load-bearing the issue is; it does not gate whether a fix is offered. Every check produces fixes.
3. Walk per item, user picks the target. Bulk-apply is reserved for purely mechanical fixes (em dashes, duplicate H1). Anything semantic — wikilink repointing, merges, routing rewrites, Plot.md generation, reorganizations — is walk-only with the user confirming the destination/winner/wording per item.
4. Two modes for every fix: apply now (executes in this run) or save to plan (writes the change as a checklist step into the plan file, whose path is resolved from the role registry in Step 4.3). User picks per finding for high-blast-radius items. Smaller fixes default to apply-now.
5. Visible progress, never silent. Step 0.5 creates one TaskCreate entry per stage and per framework; tasks update in_progress → completed as the run unfolds. The user watches the audit walk through the vault rather than waiting for one big report at the end.
6. Read and reason, don't just match. Every framework's triggers surface candidates; every finding requires the agent to read context, judge alignment with the user's stated world, and produce reasoning specific to the case. No paraphrased rule restatements as "reasoning."
7. Discover structure, never assume folder names. Vaults vary. One user's curated layer is Context/; another's is About/, Me/, frontmatter on root, or scattered across topic folders. The optimizer runs Step 1.5 (role discovery) before any framework, and every framework references roles (context-equivalent, decisions-equivalent, daily-equivalent, folder-index convention…) discovered from content — never hardcoded names. If a role is missing, it surfaces as a finding with a proposed fix ("you have no decisions-equivalent folder; here's a recommendation"), not as a silent assumption. Static path references in pass files are always abstractions; the agent resolves them through the role registry at run time.

Frameworks

#	Framework	Reference (the why)	Pass file (the how)	Applies to
F1	Anthropic CLAUDE.md	references/anthropic-claude-md.md	references/passes-anthropic-claude-md.md	every CLAUDE.md
F2	Karpathy LLM Wiki	references/karpathy-llm-wiki.md	references/passes-karpathy-wiki.md	wiki content notes
F3	Caveman compression	references/caveman-compression.md	references/passes-caveman.md	instruction-layer files
F4	Chroma context rot	references/chroma-context-rot.md	references/passes-chroma-context-rot.md	every .md
F5	Anthropic Memory	references/anthropic-managed-memory.md	references/passes-anthropic-memory.md	every .md
F6	Progressive Disclosure	references/progressive-disclosure.md	references/passes-progressive-disclosure.md	every SKILL.md
G7	General Hygiene	(project rules + practitioner notes)	references/passes-general-hygiene.md	every .md
F10	Claude 5 Rule Rewriting	references/claude-5-rules.md	references/passes-claude-5-rules.md	every CLAUDE.md, .claude/rules/, and every SKILL.md
F8	Reflection (Anthropic Dreams)	references/anthropic-dreams.md	references/passes-reflection.md	every folder where layer == "curated" in the Step 1.5 registry; reads the session-layer folders as evidence
F9	Architecture & Discoverability	references/anthropic-architecture.md	references/passes-architecture.md	whole vault — root CLAUDE.md, routing, every folder's Plot.md, the navigation chain end-to-end

When running a check, read the pass-implementation file and follow its regex / heuristic / finding format exactly. Don't paraphrase. Cite the framework reference in every finding.

Flow

1. Verify the cwd looks like a vault — light check (Step 0)
2. Create the visible task list — TaskCreate one task per stage + framework (Step 0.5)
3. Discover & classify every .md file — only technical skips (Step 1)
4. Iterate frameworks F1 → F10, applying each framework's lens with agent judgment; F10 = rule quality on the instruction layer, F8 = cross-vault synthesis, F9 = whole-vault structural reasoning + discoverability walk (Step 2)
5. Aggregate findings + write the architectural read paragraph (Steps 3 and 3.5)
6. Walk every finding through apply-now / save-to-plan — no skip option for fixes; every finding becomes an applied edit, a saved migration step, or an explicit per-item user decline (Step 4)
7. Apply approved fixes (Step 5)
8. Render HTML dashboard, save, open in browser, emit as artifact (Step 6)

---

Step 0 — Verify the cwd looks like a vault

Don't require any specific folder layout. Check (any one is sufficient):

test -f CLAUDE.md || test -f claude.md
[ "$(find . -maxdepth 4 -name 'CLAUDE.md' | head -1)" ]
[ "$(find . -maxdepth 1 -name '*.md' | wc -l)" -gt 0 ]

If none are true → stop:

This doesn't look like a markdown vault — no .md files or CLAUDE.md found. cd into your vault root and re-run.

Otherwise tell the user one line:

Auditing your vault against 10 frameworks. First I'll discover your structure (Step 1.5) — I won't assume folder names. Then I walk every fix with you. You'll see each stage as a task.

Proceed into Step 0.5.

---

Step 0.5 — Create the visible task list (TaskCreate)

This is mandatory. People running this skill on their second brain need to see what's happening — silent is unacceptable for a long-running vault audit.

Create one task per stage + one task per framework, in order. Use TaskCreate with explicit short titles. The user watches them tick through.

[ ] Discover & classify .md files (Step 1)
[ ] Role discovery — semantic folder/file classification, no hardcoded names (Step 1.5)
[ ] F1 Anthropic CLAUDE.md — read CLAUDE.md files, judge candidates
[ ] F2 Karpathy Wiki — wikilinks, orphans, schema
[ ] F3 Caveman — compression of instruction-layer files
[ ] F4 Chroma Context Rot — length, distractors, position
[ ] F5 Anthropic Memory — file size, naming, indexes
[ ] F6 Progressive Disclosure — SKILL.md layering
[ ] G7 General Hygiene — em dashes, frontmatter, H1 rules
[ ] F10 Claude 5 Rules — retired, bare prohibitions, one-sided, aggressive
[ ] F8 Reflection — cluster + judge cross-file synthesis
[ ] F9 Architecture — routing truth, Plot.md presence, discoverability walk
[ ] Aggregate findings + architectural read (Steps 3 / 3.5)
[ ] Walk every finding through apply / save-to-plan (Step 4)
[ ] Apply approved fixes (Step 5)
[ ] Render dashboard + open (Step 6)

Mark in_progress when entering a stage; completed when leaving it. For long frameworks (F2, F8, F9) emit a sub-update mid-run via TaskUpdate or a single chat line so the user knows progress.

Skipping the task list to "save time" defeats the purpose of this skill. The visible task list is non-optional.

---

Step 1 — Discover & classify every .md file

1.1 — Universal glob (every file audited)

find . -name '*.md' \
  -not -path '*/.git/*' \
  -not -path '*/.obsidian/*' \
  -not -path '*/.trash/*' \
  -not -path '*/.claude/worktrees/*' \
  -not -path '*/node_modules/*' \
  -not -path '*/dist/*' \
  -not -path '*/build/*'

No role-based skips. No "templates skipped", no "Daily skipped", no "Onboarding skipped". Every .md outside the technical skip list above gets audited against every framework rule that applies to its role. Classification routes the right rules to the right files; classification does NOT exclude files.

1.2 — Classify each file by role (first match wins) — hints only

The patterns below are hints that bias the role registry built in Step 1.5. They're not authoritative — Step 1.5 reads sample content to confirm role assignments. A file matching \d{4}-\d{2}-\d{2}\.md outside any daily-shaped folder will not be classified daily if Step 1.5 finds no daily role; it'll be a regular note.

For backwards compatibility with vaults that do use the conventional names, the patterns still apply; for vaults that don't, Step 1.5 takes over.

Role	Detection
root-claude	./CLAUDE.md or ./claude.md (cwd root only)
folder-claude	any other CLAUDE.md / claude.md in subfolders
claude-rules	files inside .claude/rules/
skill	SKILL.md files (anywhere)
index	index.md (case-insensitive)
readme	README.md (case-insensitive)
daily	matches \d{4}-\d{2}-\d{2}\.md inside any Daily/
meeting	inside *meetings*/ or filename matches \d{4}-\d{2}-\d{2} - .+\.md outside Daily/
transcript	inside *transcripts*/ or files >100KB
decision	inside *decisions*/
template	inside *templates*/ or filename ends -template.md
context	inside any Context/ (case-insensitive)
note	everything else

Build the classification map:

{
  "root_claude": "./CLAUDE.md",
  "folder_claudes": [...],
  "claude_rules": [...],
  "skills": [...],
  "indexes": [...],
  "readmes": [...],
  "dailies": [...],
  "meetings": [...],
  "transcripts": [...],
  "decisions": [...],
  "templates": [...],
  "context_files": [...],
  "notes": [...],
  "by_folder": {...},
  "stats": {"total_files": N, "total_bytes": B, "folders": F}
}

1.3 — Build supporting indexes (used by F2/F4)

Index	Built from	Used by
vault_filename_index	every .md basename, lowercased, with and without extension	F2.2, F2.4
inbound_link_index	grep across vault for `[[name(|	]
routing_table	root CLAUDE.md routing/knowledge-routing section	F2.6
top_level_entries	find . -maxdepth 1	F2.6
headers_index	per-file H2/H3 list with line numbers + byte sizes	F3.6, F5.2
protected_zones_map	per-file map of code/URL/path/frontmatter/wikilink spans	F3.x, G7.1

1.4 — Show classification summary in chat (one block, before any framework runs)

## 📋 Discovery — {N} markdown files across {F} folders, {B-formatted} total

| Role | Count |
|---|---:|
| Root CLAUDE.md | 1 |
| Folder CLAUDE.mds | {n} |
| Skills (SKILL.md) | {n} |
| .claude/rules | {n} |
| Indexes / READMEs | {n} |
| Context files | {n} |
| Notes | {n} |
| Dailies | {n} |
| Meetings | {n} |
| Transcripts | {n} |
| Decisions | {n} |
| Templates | {n} |

**Framework targets (every file in scope is audited):**
- F1 Anthropic CLAUDE.md → {n} CLAUDE.md files
- F2 Karpathy Wiki → {n} content notes (notes + context + decision + meeting + index + readme) + 1 schema doc check
- F3 Caveman → {n} instruction-layer files (CLAUDE.md + SKILL.md + .claude/rules + skill references)
- F4 Chroma Context Rot → {N} files (every `.md`)
- F5 Anthropic Memory → {N} files (every `.md`)
- F6 Progressive Disclosure → {n} skills
- G7 General Hygiene → {N} files
- F10 Claude 5 Rules → {n} instruction files (CLAUDE.md + .claude/rules + SKILL.md)
- F8 Reflection → {n} files in discovered curated-layer roles + {n} files in discovered session-layer roles ({window} window) for cross-vault synthesis
- F9 Architecture → routing table ({n} entries), {n} folders for index presence + freshness against the discovered convention, full navigation graph for discoverability, vault-specific orientation built from the discovered identity-layer

Running role discovery (Step 1.5) now…

---

Step 1.5 — Role discovery (semantic, not name-based)

This step replaces every hardcoded assumption about folder/file names. The pass files reference roles (context, projects, decisions, daily, meetings, transcripts, resources, skills, archive, identity, folder_index_convention). Step 1.5 discovers what folder/file in this vault plays each role — or records that the role is absent.

1.5.1 — How discovery works

For each abstract role, the agent does the following — in order — until something resolves:

1. Read folder names + Plot/README/index/CLAUDE files at the top level, then top-2-deep. Build a candidate list: which folders look like they could play this role based on name + their own description?
2. Read 3–5 sample files per candidate folder. Does the content match the role's purpose?
3. Score and pick. Highest-confidence candidate wins. If no candidate clears medium confidence → role is missing.

The agent does not privilege a specific folder name. Context/, About/, Me/, Personal/, Identity/, or a frontmatter section on root CLAUDE.md can all play the identity role. The agent decides by reading.

1.5.2 — Standard roles (patterns the agent recognizes)

These are patterns, not an exhaustive taxonomy. Every folder/file gets classified — these standard roles match the common shapes; anything that doesn't match becomes a custom role (Step 1.5.3).

Standard role	Default layer	What it is	How to recognize it
identity	curated	Files describing the user/operator (who they are, what they do, voice, preferences)	First-person bio content; mentions of role/title; voice or style guidelines
context	curated	Folder(s) holding canonical knowledge about the user's world (business, strategy, brand, team, stakeholders) — broader than identity	Declarative present-tense facts about the operating environment; named entities (company, products, key people)
projects	curated	Active or recent work units	Folder names matching projects mentioned in identity/context; per-folder index describing scope, status, deadlines
decisions	curated	Persistent decision records	Files with date prefixes containing decision language ("decided", "chose", "going with")
daily	session	Per-day journals or logs	Filenames matching YYYY-MM-DD\.md; folder organized by date hierarchy
meetings	session	Meeting notes	Filenames with date + person/topic; content with attendee lists, action items
transcripts	session	Raw call/voice transcripts	>100KB files with monologue/dialogue formatting
resources	curated	Reference library (prompts, frameworks, swipe files, templates)	Reusable assets, not project-specific; often nested by category
skills	curated	Skill / SOP / playbook content the user owns	SKILL.md files, or markdown describing repeatable processes/playbooks
archive	archive	Intentionally deactivated content	Folder named archive/old/deprecated/_archive, or files marked archived in frontmatter
folder_index_convention	(meta)	The user's chosen per-folder index file name	Most-frequent filename across folders that functions as an index (Plot.md, README.md, index.md, _index.md, CLAUDE.md, etc.)

1.5.3 — Custom roles (every other folder)

After standard-role discovery, every remaining top-level folder and every meaningful subfolder must be classified, not ignored. For each unclassified folder:

1. Read the folder's index file (under the discovered convention) if present.
2. Sample 3–5 files in the folder. Read first 1500 chars + headers.
3. Read the parent folder's index (if any) to see how this folder is described upstream.
4. Assign a custom role:
   • name — a slug derived from the folder name plus content (e.g., Building/ with prototype-build content → role name building; Garden/ with idea-incubation content → garden).
   • layer — one of curated (canonical, durable), session (ephemeral, time-stamped), archive (deactivated), meta (tooling, system files), unknown (agent could not confidently classify).
   • purpose — 1-line description of what the folder holds.
   • is_standard: false.
   • confidence: high | medium | low.

If the agent cannot confidently assign a layer (confidence low) → emit an F9.0 finding asking the user to clarify the folder's purpose during walk. The answer persists in the registry going forward.

Custom roles are first-class. F8, F9, and the per-finding fixers operate on roles by layer, not by membership in the standard-role list. A custom building role with layer: curated participates in F8's curated-layer synthesis exactly like the standard context role.

1.5.4 — Output: the role registry

Build this once, cache for the rest of the run, and persist to .claude/vault-roles.json at end of Step 1.5 so future runs start from confirmed assignments instead of re-prompting:

{
  "vault_root": "./",
  "discovered_at": "2026-05-08T14:23:00Z",
  "folder_index_convention": {
    "name": "README.md",
    "confidence": "high",
    "evidence": "23 of 31 non-trivial folders have README.md",
    "coverage": 0.74
  },
  "roles": [
    {"name": "identity",  "path": "./About/me.md", "kind": "file",   "layer": "curated", "is_standard": true,  "confidence": "high",   "purpose": "Operator bio + voice"},
    {"name": "context",   "path": "./Knowledge/",  "kind": "folder", "layer": "curated", "is_standard": true,  "confidence": "high",   "purpose": "Org/strategy/brand canonical knowledge"},
    {"name": "projects",  "path": "./Work/",       "kind": "folder", "layer": "curated", "is_standard": true,  "confidence": "high",   "purpose": "Active and recent work units"},
    {"name": "daily",     "path": "./Journal/",    "kind": "folder", "layer": "session", "is_standard": true,  "confidence": "medium", "purpose": "Per-day journal entries"},
    {"name": "resources", "path": "./Library/",    "kind": "folder", "layer": "curated", "is_standard": true,  "confidence": "high",   "purpose": "Prompts, frameworks, templates"},
    {"name": "archive",   "path": "./_archive/",   "kind": "folder", "layer": "archive", "is_standard": true,  "confidence": "high",   "purpose": "Deactivated content"},
    {"name": "building",  "path": "./Building/",   "kind": "folder", "layer": "curated", "is_standard": false, "confidence": "high",   "purpose": "Active prototype builds and experiments"},
    {"name": "garden",    "path": "./Garden/",     "kind": "folder", "layer": "curated", "is_standard": false, "confidence": "medium", "purpose": "Long-form essays in slow incubation"},
    {"name": "inbox",     "path": "./Inbox/",      "kind": "folder", "layer": "session", "is_standard": false, "confidence": "high",   "purpose": "Unprocessed capture; aged out into Garden or Resources"}
  ],
  "missing_standard_roles": ["decisions", "meetings", "transcripts"],
  "low_confidence_roles": ["garden"],
  "unconfirmed_custom_roles": []
}

1.5.5 — Show the discovery summary in chat (one block)

Frame this as "here's the structure I see in your vault" — not "here's what's missing from a checklist." The user's structure is the source of truth; the reference taxonomy is just one of the lenses the agent uses to recognize patterns.

## 🔍 Your vault structure — {N_folders} folders classified

| Folder | Role | Layer | Purpose | Confidence |
|---|---|---|---|---|
| ./About/me.md | identity | curated | Operator bio + voice | high |
| ./Knowledge/ | context | curated | Org/strategy/brand | high |
| ./Work/ | projects | curated | Active and recent work | high |
| ./Journal/ | daily | session | Per-day journal | medium |
| ./Library/ | resources | curated | Prompts, frameworks, templates | high |
| ./_archive/ | archive | archive | Deactivated content | high |
| ./Building/ | building (custom) | curated | Active prototype builds | high |
| ./Garden/ | garden (custom) | curated | Long-form essays in slow incubation | medium |
| ./Inbox/ | inbox (custom) | session | Unprocessed capture | high |

**Folder-index convention I detected:** README.md (74% coverage)

I'll audit this structure as it stands. F9.0 may suggest specific structural improvements where I see concrete evidence they'd help your vault (not just because the reference taxonomy contains them) — you'll review each suggestion in walk. Confirmed assignments persist to `.claude/vault-roles.json`.

Running F1 now…

The summary frames what the user has first. F9.0 findings about gaps appear later in the walk, with reasoning grounded in observed problems — not as a deficiency table at discovery time.

1.5.6 — Hard rules for downstream frameworks

• Frameworks reference roles by layer, not by name. F8's curated layer = every role with layer == 'curated' (standard or custom). F8's session layer = every role with layer == 'session'. F9 walks every folder regardless of role membership.
• Custom roles participate in every framework that operates on their layer. If building is layer: curated, F8 looks at Building/ for merge candidates, contradictions, themes, and promotions exactly like Context/.
• Missing roles never block a framework. If decisions is missing, F8 proceeds without it; F9.0 produces a finding suggesting the user create one (or assign the role to an existing custom folder).
• The folder-index convention is what F9.2 enforces — not Plot.md by default. If the user's vault uses README.md, F9.2 generates/refreshes README.md. If no convention exists, F9.0 proposes adopting one.
• Persisted registry is read at the start of Step 1.5. If .claude/vault-roles.json exists from a prior run, the agent loads it as the baseline and only re-classifies new folders or folders the user flagged for re-review. Confirmed assignments don't re-prompt every run.
• No framework hardcodes folder paths or file names. Examples in pass files are illustrative; runtime resolves through the registry.

---

Step 2 — Iterate frameworks F1 → F10 with judgment

This is not a regex pass. For each framework, read its pass-implementation file, then apply every check it defines to the files in that framework's scope. Triggers in the pass files surface candidates; the agent reads context and judges each candidate before producing a finding. Every finding includes reasoning specific to the case.

Why: a regex match on \bjust\b flags "just run X" (where "just" is doing real work — contrasting with running multiple) the same as "It's just a quick check" (where it's filler). Only an agent reading the line in context can tell which is which. The same applies to "be careful" (sometimes a closing reminder, sometimes a vague platitude), IMPORTANT: (sometimes earned, sometimes inflation), voice.md + brand.md (sometimes overlapping, sometimes intentionally separated), and most other framework signals.

2.1 — For each framework F1, F2, F3, F4, F5, F6, G7, F10, F8, F9 (in this order)

F10 runs after G7: it is file-local like F1–G7 and shares their targets, so it belongs with them rather than with the whole-vault passes. F8 runs second-to-last (cross-file synthesis). F9 runs last because it consumes the structural picture F1–G7 produced and operates on the largest blast radius (whole-vault structural reasoning, Plot.md generation, reorg proposals). Running them last keeps fix application ordered smallest-to-largest in Step 5.