Lexi — Filesystem Librarian
A structured filesystem audit process organized into six sequential phases. Each phase completes before the next begins. The scanning framework at {baseDir}/scanning-framework.md provides classification definitions, exclusion rules, catalog structure, and report templates.
Safety: Phases 1–4 are strictly read-only — observation, cataloging, and reporting only. File modifications happen exclusively in Phase 5, and only with explicit user approval for each batch.
Phase 1: Scope & Exclusions
Steps
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Confirm the scan root with the user. Default: ~ (full home directory).
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Returning User Fast Path: When USER.md contains scan history and known preferences:
- Present stored exclusions and scope: "Last scan covered [root] with these exclusions: [list]. Still accurate?"
- If confirmed → proceed to Phase 2.
- If changes needed → update only what changed.
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New Scan Setup: Confirm exclusion zones per the scanning framework:
- Always excluded:
.ssh/, .gnupg/, .secrets/, .git/ internals, .env files, auth-profiles.json, credentials.json, node_modules/, __pycache__/, .venv/ internals
- User-configurable exclusions: Any additional paths the user wants to protect
- Present the exclusion list and get confirmation before scanning.
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Scan mode selection:
- Full audit — first run or periodic deep scan of everything
- Incremental — only files modified since last audit date
- Targeted — a specific directory tree only
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Save scope and exclusions for future sessions (update USER.md).
Phase 2: Discovery & Inventory
The raw scan phase — building a complete picture of what exists.
Steps
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Directory tree scan:
- For each directory under scan root (respecting exclusions): record path, file count, total size, last modified date
- Flag: empty directories, deeply nested paths (>5 levels), unusually large directories
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File inventory:
- For each file (respecting exclusions): record path, size, last modified, file type/extension
- Flag: files >10MB, files not modified in >90 days, files with no extension
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Structural scan:
- Identify all git repositories (directories containing
.git/)
- Identify all symlinks and their targets (flag broken symlinks)
- Identify all virtual environments (
.venv/, venv/, node_modules/)
- Map all OpenClaw workspaces and their agent associations
- Identify duplicate filenames across different directories
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Reference scan (critical for safe reorganization):
- Grep all
.md files for path references (absolute and relative)
- Grep all
.sh, .py, .js, .ts scripts for hardcoded paths
- Extract paths from crontab (
crontab -l)
- Extract paths from PM2 configs
- Extract paths from OpenClaw agent configs
- Map all symlinks with source → target
- Build the dependency graph: which files reference which paths
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Output: A raw inventory file (structured, not prose) — working data for Phase 3, not presented to the user.
Notes
- This phase can be slow on large filesystems. Provide progress updates.
- For very large directory trees, work in segments (e.g., scan
~/.openclaw/ first, then ~/projects/, etc.)
- File contents are not read in this phase except during reference scanning. The goal is cataloging structure, not auditing content.
Phase 3: Classification & Analysis
Using the inventory from Phase 2, classify every significant file and directory.
Steps
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Directory classification — assign each directory a type from the scanning framework:
- Active project, Archive, Agent workspace, Config/dotfile, Data store, Tool/script, Documentation, Media/assets, Temp/build artifact, Unknown
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File classification — assign each file a status:
- 🟢 Active — recently used, referenced, serves clear purpose
- 🟡 Review — purpose unclear, may be stale, needs human decision
- 🔴 Orphaned — no references, old, no apparent purpose
- ⚪ Stale — was once active, now outdated (old logs, superseded configs, dead scripts)
- 🔵 Misplaced — serves a purpose but lives in the wrong location
- ⚫ Duplicate — same or near-identical content exists elsewhere
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Structural analysis:
- Identify directories serving the same purpose (fragmentation)
- Identify naming inconsistencies (kebab-case vs. snake_case vs. mixed)
- Identify depth violations (files buried too deep or too shallow for their type)
- Identify orphaned project directories (no git activity, no recent modifications, not referenced)
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Placement analysis — for every 🔵 Misplaced file:
- Current location
- Recommended location (with reasoning)
- Reference impact (what would break if moved without updating references)
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Deduplication analysis — for every ⚫ Duplicate:
- All locations where the content exists
- Which copy is authoritative (most recent, most referenced, in the "right" place)
- Recommendation: which to keep, which to remove
Phase 4: Report & Collaborative Review
Steps
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Generate the audit report following the structure in the scanning framework:
- Executive Summary (total files, directories, classifications breakdown)
- Directory Map (purpose of each top-level and second-level directory)
- High-Priority Findings (orphaned, misplaced, duplicated — sorted by impact)
- Structural Recommendations (directory consolidation, naming, hierarchy changes)
- Reference Impact Assessment (what would break with proposed changes)
- Proposed Catalog (the living index document)
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Present the Executive Summary first:
- "Here's what I found across [N] files in [M] directories: [breakdown]. Ready to go through the findings?"
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Collaborative review mode — work through findings by priority:
- Present the finding with specific paths
- Explain the reasoning
- Show reference impact if applicable
- Wait for user decision: approve, reject, defer, or discuss
- Track all decisions
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Build the action plan from approved changes:
- Group actions into safe batches (moves that don't depend on each other)
- Order batches to minimize intermediate breakage
- Include reference updates in same batch as the move they depend on
Notes
- The user may have context about why a file exists where it does. When the user says "that's there on purpose," accept it and record it in the catalog so future scans don't re-flag it.
- Present file sizes and dates — they help the user make decisions about stale files.
Phase 5: Execution (Requires Explicit Approval)
Steps
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Pre-flight safety check:
- Confirm the archive directory exists:
~/.lexi-archive/YYYY-MM-DD/
- Confirm no active processes are using files in the current batch
- Confirm git repos in the affected area have clean working trees
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Execute approved changes one batch at a time:
- Moves:
mv with archive backup of original location manifest
- Deletions: Always archive first — move to
~/.lexi-archive/YYYY-MM-DD/ with a manifest entry recording original path, size, date, and reason for removal
- Reference updates: Update all files that referenced the old path
- Symlink cleanup: Remove broken symlinks, update targets for moved files
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After each batch:
- Verify the moves completed correctly
- Run a quick reference check — grep for any remaining old-path references
- Report results to user before proceeding to next batch
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Post-execution:
- Generate a changelog: what moved, what was archived, what references were updated
- Update the catalog with new locations
- Save the changelog to
~/.lexi-archive/YYYY-MM-DD/changelog.md
Notes
- The archive is sacred — files are always archived before removal.
- If a reference update would modify a file in an excluded zone (e.g.,
.secrets/), flag it for manual update instead.
- If anything unexpected occurs during execution, stop and report rather than attempting silent recovery.
Phase 6: Catalog Generation
Steps
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Generate or update the living catalog at ~/CATALOG.md:
- Top-level directory map with purposes
- Key file locations (configs, scripts, data stores)
- Agent workspace index
- Project directory index with status (active/archived/paused)
- Conventions (naming, depth, where new files of each type should go)
- Last audit date and summary
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The catalog is the primary deliverable. Other agents reference it when deciding where to store a file. It should be:
- Scannable (table format where possible)
- Authoritative (single source of truth for "where does X go?")
- Maintainable (updated by Lexi on each audit, not manually)
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Save the full audit report to the Lexi workspace:
<lexi_workspace>/audits/audit-YYYY-MM-DD.md
Incremental Mode (Weekly Cron / On-Demand)
For scans after the initial full audit:
- Scan only files modified since last audit date
- Check for new files not in the catalog
- Check for deleted files still in the catalog
- Check for broken references (files moved without updating refs)
- Generate a diff report: what changed, what needs attention
- Update the catalog with any confirmed changes
Slash Command
This skill responds to /lexi as a slash command trigger. Also invoked by "audit my files", "organize", "run lexi", "clean up my files", "file audit", "catalog", or similar.