Brain

Brain

Unified skill for all operations on jonmagic's second brain repository (~/Brain). Covers searching, creating files, capturing content, committing changes, and loading context.

When to Use

Use this skill when the user wants to do anything with the Brain. Common triggers:

The user may also say /brain <anything> as a convenience.

Common Patterns

These patterns are shared across all operations. They are defined here once and referenced throughout.

Git Sync

Before reading or writing any Brain content, sync from remote:

cd ~/Brain && git pull --rebase --autostash

If the pull fails with a merge conflict, abort and report — do NOT auto-resolve:

cd ~/Brain && git rebase --abort

Then tell the user about the conflict so they can resolve it manually. Never use -X theirs or -X ours — these strategies can silently destroy data on frequently-edited files like Weekly Notes.

If the pull fails for a non-conflict reason (network error, etc.), warn and proceed with local state.

Frontmatter & TIDs

All new Brain markdown files require YAML frontmatter:

---
uid: <TID>              # Required. 13-char base32-sortable timestamp ID
type: <collection>      # Required. See collection types below
created: <ISO 8601>     # Required. When the content was created
tags: []                # Optional. Controlled vocabulary (see .brain/tag-vocabulary.md)
links:                  # Optional. Structured relationships
  parent: []
  source: []
  related: []
---

Collection types: daily.project, weekly.note, meeting.note, project, snippet, transcript, executive.summary, bookmark, archive, reference

Generate a TID:

ruby ~/.copilot/skills/brain/scripts/generate-tid.rb

Add frontmatter to an existing file:

ruby ~/.copilot/skills/brain/scripts/add-frontmatter.rb <file>

Options: --dry-run, --type <type>, --created <date>, --force (adds missing fields to existing frontmatter)

Timestamp detection: If the path contains YYYY-MM-DD, that date is used for created. Otherwise, file mtime is used. The script is idempotent — existing frontmatter is not modified unless --force is passed.

Tags: Consult .brain/tag-vocabulary.md before assigning. Pick 1-4 specific tags per file. Tags span six categories: Work Projects, Technical Domains, Activities, Teams, Personal, and Meta.

File Numbering

Many Brain directories use dated folders with sequential numbering:

<Directory>/YYYY-MM-DD/
  01 first topic.md
  02 second topic.md
  03 third topic.md

When creating files: check the folder for the highest existing number and increment. Create the date folder if it doesn't exist.

Wikilinks

Use Obsidian-style wikilinks to connect documents:

• [[Daily Projects/2026-02-02/05 threadwaste questions evidence.md]]
• [[Projects/hamzo/executive summary]]
• [[uid:TID|Display Text]]

Operations

Search & Index

Search and query the Brain's structured index. Supports full-text search, tag filtering, type filtering, link traversal, timeline views, and recent file discovery.

Build the index first (takes 2 seconds, produces `/Brain/.brain/index.json`):

ruby ~/.copilot/skills/brain/scripts/brain-index.rb ~/Brain --stats

Search modes:

# Full-text search (titles, summaries, paths, tags)
ruby ~/.copilot/skills/brain/scripts/brain-search.rb "proxima abuse"

# Tag search
ruby ~/.copilot/skills/brain/scripts/brain-search.rb --tag hamzo

# Type filter (combinable with tag)
ruby ~/.copilot/skills/brain/scripts/brain-search.rb --type daily.project --tag proxima

# Timeline view (chronological evolution of a topic)
ruby ~/.copilot/skills/brain/scripts/brain-search.rb --timeline "nuanced-enforcement"

# Link traversal (find everything linking to a UID)
ruby ~/.copilot/skills/brain/scripts/brain-search.rb --linked-to 3lz7nwvh4zc2u

# Recent files (modified in last N days)
ruby ~/.copilot/skills/brain/scripts/brain-search.rb --recent 7

# Index statistics
ruby ~/.copilot/skills/brain/scripts/brain-search.rb --stats

Options: --tag <tag>, --type <type>, --linked-to <uid>, --timeline <query>, --recent <days>, --limit <n> (default: 20), --compact (paths only), --index <path>, --stats

Context Loading

Load relevant Brain content at session start. Use when starting work on a project/topic, preparing for a meeting, or answering "what do I know about X?"

Workflow:

1. Sync — cd ~/Brain && git pull --rebase --autostash
2. Rebuild index — ruby ~/.copilot/skills/brain/scripts/brain-index.rb ~/Brain
3. Search — by keyword, tag, type, or timeline depending on what the user needs
4. Read key files in priority order:
   • Project executive summary (Projects/<slug>/executive summary.md)
   • Recent Daily Projects on the topic
   • Connected files from other time periods

Quick context for a known project:

ruby ~/.copilot/skills/brain/scripts/brain-index.rb ~/Brain
cat ~/Brain/Projects/<slug>/executive\ summary.md
ruby ~/.copilot/skills/brain/scripts/brain-search.rb --tag <project-tag> --type daily.project --limit 5

Commit & Push

Analyze Brain changes, create semantic commits, and push. Non-interactive — do the best job without asking for confirmation.

Workflow:

1. cd ~/Brain
2. Sync from remote (see Common Patterns)
3. git status to see changes
4. Group files by type/purpose and create commits:

5. git push after all commits
6. Report what was committed

Safety rules:

• Never auto-resolve merge conflicts
• Never force push
• Never amend commits unless explicitly asked
• Show what will be committed but do not pause for confirmation

Auto-commit cron (scripts/auto-commit.sh): Hourly safety net that commits and pushes uncommitted changes. Install with crontab -e:

0 * * * * ~/.copilot/skills/brain/scripts/auto-commit.sh

Create Daily Project Note

Create a numbered markdown file in today's Daily Projects/YYYY-MM-DD/ folder.

Workflow:

1. Sync from remote
2. User provides a title/description
3. Create Daily Projects/YYYY-MM-DD/ folder if needed
4. Find next available number prefix (01, 02, ...)
5. Create NN title.md with frontmatter:

---
uid: <TID>
type: daily.project
created: <date folder date>T00:00:00Z
session: <agent resume command>
---

# title

Session auto-detection for the session frontmatter field:

Run ruby ~/.copilot/skills/brain/scripts/detect-session.rb --project-dir ~/Brain to detect. If it exits non-zero, omit the session field.

Create Bookmark

Save a URL as a dated bookmark file with structured frontmatter and an executive-summary-style narrative body.

File format: Bookmarks/YYYY-MM-DD/NN title.md

---
uid: <TID>
type: bookmark
created: <date>T00:00:00Z
url: https://example.com/article
title: "Article Title"
source: hacker-news
tags: [pkm, architecture]
---

Workflow:

1. Sync from remote
2. Extract URL(s) from user message
3. Get optional context: blurb, source (e.g. hacker-news, slack), tags
4. Fetch page title via WebFetch
5. Generate body: user's blurb if provided, otherwise generate executive-summary-style narrative
6. Create file with frontmatter + body
7. Confirm to user

Body rules (when generating, not when user provides blurb):

1. Start with a clear title line (not a markdown header)
2. Narrative paragraphs only — no bullets, headers, or lists
3. Contextual linking: link to source when referencing claims. For GitHub: @username unlinked, with separate ([ref](URL)) links
4. Focus on critical content: key arguments, evidence, implications, business impact
5. Close with personal relevance paragraph
6. Formal tone, dense prose

If fetch fails or returns thin metadata, still create the bookmark with a short narrative based on title/URL.

Multiple URLs: Create one file per URL with sequential numbering.

Create Weekly Note

Create a weekly planning note from template with dates filled in, then interactively review carryover items from last week.

Workflow:

1. Sync from remote
2. Run: ~/.copilot/skills/brain/scripts/create-weekly-note
3. Review previous week's Active Projects — confirm what's still active
4. Review unchecked items from previous week's Parked, Sessions, TODO sections:
   • Mark done, keep for this week, or drop
5. Copy confirmed carryover items to new note
6. Add frontmatter:

---
uid: <TID>
type: weekly.note
created: <Sunday date ISO 8601>
tags: []
links:
  related: []
---

Template: Edit assets/weekly-note-template.md to customize. Placeholders: {{sunday:YYYY-MM-DD}} through {{saturday:YYYY-MM-DD}}. The default recurring schedule includes {{Meeting Notes/tgthorley}} on Tuesdays at 1400.

Archive Meeting

Archive meeting transcripts (Zoom folders or Teams .vtt files) into structured Brain artifacts.

Outputs:

• Transcripts/YYYY-MM-DD/NN.md — imported transcript
• Executive Summaries/YYYY-MM-DD/NN.md — generated summary
• Meeting Notes/<target>/YYYY-MM-DD/NN.md — meeting notes
• Weekly note checkbox marked complete

Workflow — use the CLI:

archive-meeting \
    --brain-dir ~/Brain \
    --executive-summary-prompt-path ~/code/jonmagic/prompts/summarize/zoom-transcript-executive-summary.md \
    --detailed-notes-prompt-path ~/code/jonmagic/prompts/summarize/transcript-meeting-notes.md

Interactive mode uses fzf to select from recent meetings and pending meeting note targets.

Explicit mode (when user specifies input and target):

archive-meeting \
    --brain-dir ~/Brain \
    --input "/path/to/transcript.vtt" \
    --meeting-notes-target "jonmagic" \
    --executive-summary-prompt-path ~/code/jonmagic/prompts/summarize/zoom-transcript-executive-summary.md \
    --detailed-notes-prompt-path ~/code/jonmagic/prompts/summarize/transcript-meeting-notes.md

CLI options: --brain-dir, --input, --meeting-notes-target, --executive-summary-prompt-path, --detailed-notes-prompt-path, --date, --dry-run

Prerequisites: The archive-meeting CLI from ~/code/jonmagic/scripts must be on PATH. Verify with which archive-meeting.

Frontmatter for outputs: Add to any files the CLI doesn't frontmatter automatically. Link executive summaries and meeting notes back to their transcript via links.source: [<transcript TID>].

References: references/formats.md (Zoom/Teams conventions), references/meeting_notes_routing.yml (routing overrides)

Archive Session

Archive a Copilot CLI session to the Brain — creates a daily project file with the session transcript and adds a resume link to the weekly note.

Inputs needed: Session ID (from session context path ~/.copilot/session-state/UUID/) and focus (1-5 word description from user).

Workflow:

1. Sync from remote
2. Ask user for the focus
3. Extract transcript:

   ~/.copilot/skills/brain/scripts/extract-transcript \
     --session-id "SESSION_ID" \
     --output "/tmp/session-transcript.md"
   

4. Create daily project file:

   ~/.copilot/skills/brain/scripts/create-daily-project \
     --focus "FOCUS" \
     --session-id "SESSION_ID" \
     --transcript "/tmp/session-transcript.md"
   

5. Add frontmatter to created file:

   ruby ~/.copilot/skills/brain/scripts/add-frontmatter.rb "PATH_FROM_STEP_4"
   

6. Update weekly note:

   ~/.copilot/skills/brain/scripts/update-weekly-note \
     --focus "FOCUS" \
     --session-id "SESSION_ID" \
     --daily-project-path "PATH_FROM_STEP_4"
   

7. Report the daily project path and which weekly note was updated

Catch Me Up

Synthesize daily activity (daily projects, meeting notes, GitHub issues/PRs) into narrative summaries for weekly note day sections. Fills gaps where the user didn't write context notes.

Workflow:

1. Sync from remote
2. Determine date range:
   • "this week" → current week (Sunday through today)
   • "last week" → previous full week
   • "catch me up" with no qualifier → current week
3. Read the weekly note — identify which day sections need filling:
   • A day has substantive content only if it has narrative bullets (sentences describing what happened)
   • Just wikilinks, session commands, or - placeholders do NOT count
4. Gather activity:

   ~/.copilot/skills/brain/scripts/gather-activity --week YYYY-MM-DD --lines 100
   

   Options: --date, --from/--to, --files (paths only), --no-github, --github-user <user>
5. Read full content of daily projects and meeting notes for days needing summaries
6. Write first-person narrative bullets under each day heading

GitHub activity classification — critical rules:

The gather-activity script classifies GitHub items into summary-safe and context-only:

• issues / pull_requests arrays → safe to summarize (created or merged that day)
• context_only_issues / context_only_pull_requests → advisory only, ignore unless corroborated by daily project or meeting note

Activity kind rules:

Validation gate: Never write "opened", "filed", "merged", "shipped", "reviewed" or similar day-specific language unless backed by a summary-safe GitHub item or corroborating daily project / meeting note. Fail closed on ambiguity.

Voice and format:

• First person, informal, concise
• Short bullet points (one line each)
• Capture what was worked on, key decisions, what happened
• Include meeting highlights: who, key outcomes
• Include session resume commands from daily project frontmatter
• Link to daily project files with wikilinks
• Tone: quick capture of state of mind and progress, like end-of-day notes

Good example:

## Monday
- rescheduled with znull to next week to talk about the abuse data plane idea
- attended team sync
- synced with romanofoti
- started the morning by getting spamurai-next and hamzo PRs closer to shipping

Avoid: listing just file/meeting names, corporate language, bold prefixes, fabricating information.

Day heading formats: Day section headings may use either ## Monday or ## Monday (2026-02-09). Match whichever format the existing note uses.

Options: Augment existing days, specific days only, dry run, multi-week ranges.

Brain Reference

Directory Map

Append-Only Discipline

• Weekly Notes, Meeting Notes: New entries at top (reverse-chronological)
• Daily Projects: Append running log to bottom
• Snippets, Executive Summaries: Create new files for new time periods

Before Editing Existing Notes

1. Scan the last few entries to understand current state
2. Check for linked documents that provide context
3. Maintain chronological or thematic continuity
4. If a concept exists elsewhere, link to it rather than restating

File Creation Decision Tree

1. Daily execution work? → Daily Projects/YYYY-MM-DD/
2. Weekly planning? → Weekly Notes/Week of YYYY-MM-DD.md
3. Meeting record? → Meeting Notes/<person-or-team>/YYYY-MM-DD/
4. Multi-week initiative? → Projects/<slug>/
5. External link to save? → Bookmarks/YYYY-MM-DD/
6. Transcript? → Transcripts/YYYY-MM-DD/
7. Leadership summary? → Executive Summaries/YYYY-MM-DD/
8. Accomplishment tracking? → Snippets/
9. When in doubt: Start in Daily Projects/ and migrate later.

Script Reference

All scripts live in ~/.copilot/skills/brain/scripts/.