BYOAO Guide

Workflows

7 min read

Workflows

Real scenarios showing how to use BYOAO day-to-day. Each workflow introduces the relevant skills in context.

1. First Cook — Compiling Your Notes

When: You’ve just created your KB and have some notes (imported or freshly written).

Steps:

  1. Make sure your vault is open in Obsidian with CLI enabled
  2. Open the Agent Client panel
  3. Run /prep to enrich frontmatter across your notes
  4. Run /cook to compile knowledge from your notes
  5. Review the summary of changes
  6. Press Cmd+G to see the graph

What to expect:

  • Entity pages created for people, projects, and products mentioned across notes
  • Concept pages for methods, rules, and decisions
  • Contradictions detected and flagged for review
  • INDEX.base and log.md updated
  • A summary like: “Created 5 entity pages, 3 concept pages. 1 contradiction flagged.”

Tips:

  • Run /cook on a few core notes first (use /cook "topic name") to see how it works
  • Re-run /cook anytime — it’s incremental (only processes new/modified notes)
  • After /cook, run /health to check for issues

2. Organizing After Cook — Restructuring Your Vault

When: You’ve run /prep and your notes now have frontmatter, but files are scattered across a messy directory structure (common when adopting an existing knowledge base).

Steps:

  1. Make sure you’ve already run /prep (the agent needs type metadata to decide where files belong)
  2. Run /organize to see the proposed directory restructuring
/organize                    # Full vault analysis
/organize dry-run            # Preview changes without executing
/organize scope=Projects/    # Focus on a specific folder
  1. Review the before/after summary — the agent groups moves by action (e.g. “Move 12 meeting notes to Meetings/”)
  2. Approve or adjust — you can accept all, reject all, or cherry-pick moves
  3. The agent uses obsidian move for each file, which automatically updates all wikilinks

What to expect:

  • Files reorganized by type based on frontmatter metadata
  • Coherent groups stay together (a sprint folder with related files won’t be split up)
  • All wikilinks and backlinks update automatically — no broken references

Tips:

  • Start with dry-run to see what would change before committing
  • Use scope= to reorganize one folder at a time for more control
  • The agent won’t move files where the benefit is unclear — it’s conservative by default

3. Weekly Review — Keeping the Knowledge Base Fresh

When: You’ve been writing notes all week and want to integrate them into the knowledge base.

Steps:

  1. Run /cook to compile this week’s notes into knowledge
  2. Run /health to audit agent pages
/cook
/health

What /health reports:

  • Orphan pages (not connected to anything)
  • Broken wikilinks (links to non-existent notes)
  • Stale content (outdated agent pages)
  • Frontmatter violations
  • Tag taxonomy drift

Follow-up actions:

  • For orphan pages: decide if they should be connected or archived
  • For broken links: fix the link or create the missing page
  • For stale content: /cook will update on the next run

4. Tracing an Idea — How Did My Thinking Evolve?

When: You want to understand how a concept developed across your notes over time.

Example: You’ve been thinking about “API rate limiting” for months and want to see the full arc.

Steps:

/trace topic="rate limiting"

What you get:

  • A chronological timeline of every note that mentions “rate limiting”
  • Phases identified: Discovery → Investigation → Decision → Implementation
  • Turning points flagged: “After reading System Design Doc, your approach changed”
  • Open threads: “You explored token buckets but never followed up after June”

When to use:

  • Before making a decision — see what you’ve already explored
  • When writing a retrospective — trace a project’s evolution
  • When onboarding someone — “here’s how this decision was made”

5. Bridging Two Topics — Finding Hidden Connections

When: You suspect two topics are related but can’t articulate how.

Example: You work on “payment processing” and “user onboarding” separately. Are they connected in your vault?

Steps:

/connect from="payment processing" to="user onboarding"

What you get:

  • Shared notes — notes that discuss both topics
  • Shared people — people involved in both areas
  • Graph paths — how the two topics connect through intermediate notes (up to 3 hops)
  • Strength assessment — strong, moderate, or weak connection
  • Suggested actions — specific notes to link, hub notes to create

When to use:

  • Cross-team collaboration — “how does my work connect to yours?”
  • Strategic thinking — “what ties these initiatives together?”
  • Writing — “I need to explain how A relates to B”

If no connection is found: That’s a useful result too. It means these topics haven’t intersected in your notes yet — maybe they should, maybe they shouldn’t.

6. Generating Ideas — What Should I Work On Next?

When: Your vault has substantial content and you want creative, actionable suggestions.

Steps:

/ideas
/ideas focus="infrastructure"   # Focus on a domain

What you get:

  • Synthesis ideas — combine two existing threads into something new
  • Gap ideas — something the vault implies is needed but doesn’t exist
  • Connection ideas — two people/projects that should be talking
  • Amplification ideas — take something small and scale it
  • Challenge ideas — question an assumption the vault takes for granted

Every idea cites 2+ vault notes and includes a concrete next step.

When to use:

  • Quarterly planning — “what opportunities does my vault reveal?”
  • Feeling stuck — let the vault suggest what to work on
  • Cross-domain innovation — find overlap between separate areas

7. Challenging a Belief — Am I Right About This?

When: You’re about to make a big decision and want to test it against your own history.

Example: You believe “we should migrate to microservices.”

Steps:

/challenge belief="we should migrate to microservices"

What you get:

  • Supporting evidence from your notes (fair assessment first)
  • Counter-evidence: contradictions, position changes over time
  • Unstated assumptions your belief relies on
  • Missing perspectives (whose viewpoint is absent?)
  • Confidence rating: Strong / Moderate / Weak / Contradicted

When to use:

  • Before major decisions — “does my vault support this?”
  • Resolving disagreements — “what do my own notes say?”
  • Retrospectives — “was this the right call?“

8. Detecting Drift — Am I Doing What I Said I Would?

When: You want to compare your stated plans with what actually happened.

Steps:

/drift                         # Last 30 days
/drift period=60d              # Last 60 days
/drift focus="API migration"   # Focus on a project

What you get:

  • Each intention categorized: aligned, delayed, drifted, abandoned, or emergent
  • Pattern detection: priority displacement, scope creep, goal abandonment
  • Emergent work recognized (unplanned but important)
  • Questions to consider (descriptive, not judgmental)

When to use:

  • End of sprint/month — “did I follow through?”
  • Quarterly review — “where did my priorities actually go?”
  • When overwhelmed — “what’s consuming my attention vs what I planned?“

9. Capturing Web Content — From Browser to Knowledge Base

When: You read articles, research papers, documentation, or anything online that’s relevant to your work.

Setup: Install Obsidian Web Clipper for your browser. See Getting Started → Web Clipper for template setup.

Steps:

  1. Find an article or page worth keeping
  2. Highlight key passages (optional — highlights are preserved in the clipping)
  3. Click the Web Clipper icon → clip to your vault
  4. The page saves as Markdown with frontmatter in your Clippings/ folder
/cook
  1. On the next /cook cycle, the AI reads your clippings alongside your own notes
  2. Entities, concepts, and connections from the clipped content get compiled into the knowledge base

What to expect:

  • Clipped articles treated as source material, same as your handwritten notes
  • People, companies, and concepts mentioned in articles get entity/concept pages
  • The sources field on compiled pages links back to the original clipping
  • Contradictions between clipped content and existing knowledge get flagged

Tips:

  • Set up auto-apply rules in Web Clipper for different sites (articles, papers, recipes)
  • Clip liberally — /cook is incremental, so new clippings are processed on the next run
  • Use highlights to mark the most important passages; they’re visible when you revisit the page

Building a Routine

Here’s a rhythm that works well:

FrequencyActionSkill
DailyWrite a daily note, capture meetings and ideas—
While browsingClip useful articles and references to the vaultWeb Clipper
WeeklyCompile new notes + clippings, audit health/cook + /health
After cookRestructure directories if needed/organize
When curiousTrace how a topic evolved/trace
QuarterlyGenerate ideas, review drift/ideas + /drift
Before big decisionsPressure-test your assumptions/challenge
As neededBridge two topics you’re working on/connect

The goal is not to run every skill every day. Write freely, cook weekly, think quarterly.

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