Collections

mks search '"testosterone dose" -study' --limit 5 --snippets
mks search "sleep* recovery" --limit 5 --snippets --collection notes

Filter by frontmatter

# Note: flag is --where-clause (not --where)
mks search "recovery" --where-clause "category=health" --limit 5 --snippets
mks search "RCT" --where-clause "type=RCT" --collection literature --limit 5 --snippets
mks search "paper" --where-clause "date>2024-01" --limit 5 --snippets

Supported fields: collection, path, title, or any YAML frontmatter key. Operators: = != > < >= <=

Semantic search (requires Ollama)

# Only if Ollama is running — falls back to BM25 if not
mks embed                              # generate embeddings first (one-time)
mks search "vec: how does creatine increase strength" --limit 5
mks search "vec: recovery protocols after heavy training" --collection notes

Ollama not currently installed. To enable: ollama pull nomic-embed-text then mks embed.

Intent prefix (disambiguation)

mks search 'intent: looking for notes on testosterone therapy, not general biology' \
  --limit 5 --snippets

Retrieve

mks get <id>              # full document content (id from search results)
mks list --limit 20
mks list --collection notes --limit 50
mks stats

Graph

# Build/rebuild graph (run after adding new docs)
mks graph build
mks graph build --force    # re-extract all

# Traverse from a concept
mks graph query "creatine"                    # BFS depth 2, 2000-token budget
mks graph query "testosterone" --depth 3 --budget 4000

# Find connections
mks graph path "creatine" "mTOR"              # shortest path between two nodes
mks graph neighbors "testosterone" --depth 2
mks graph backlinks "mTOR"                    # what links TO this node
mks graph god-nodes --limit 20               # most connected nodes in KB

# Overview
mks graph report

Workflow for answering a question

1. search (2-3 queries)  →  2. get full docs  →  3. synthesize

# Multiple angles on same topic
mks search "sleep quality protocols" --limit 3 --snippets --collection notes
mks search "circadian rhythm optimization" --limit 3 --snippets --collection notes
mks search '"sleep debt" recovery' --limit 3 --snippets --collection notes

# Get the most relevant doc in full
mks get <id>

Adding new content

# Single file
mks add ~/projects/knowledge/notes/health/enhancers/perform/new-compound.md --collection notes

# Directory
mks add ~/projects/knowledge/notes/pharmacology/ --collection notes

# Re-ingest changed files
mks add ~/projects/knowledge/notes/ --force --collection notes

# Web page
mks add https://examine.com/supplements/creatine/ --collection notes

# Watch for live updates
mks watch ~/projects/knowledge/notes/ --collection notes

# After adding — rebuild graph
mks graph build

PDF → KB pipeline (with cnv)

cnv paper.pdf -f raw -o /tmp/out/
mks add /tmp/out/paper.md --collection literature
mks embed                    # if Ollama running
mks graph build

Domain map

health/
  enhancers/perform/    # creatine, caffeine, beta-alanine, nitrates
  enhancers/recover/    # sleep aids, anti-inflammatories
  enhancers/think/      # nootropics, cognitive enhancers
  enhancers/feel/       # mood, wellbeing
  hormonal-management/  # TRT, SARMs, aromatase
  exercise/             # training protocols, hypertrophy, periodization
  nutrition/            # macros, timing, metabolic health
  lifestyle/            # sleep, stress, circadian
  specialised/          # specific performance protocols

pharmacology/           # drug mechanisms, PK/PD, dosing, toxicology
human-biology/          # anatomy, physiology, endocrinology, pathology

When to search

Always search when the question involves:

• Supplements, ergogenics, nootropics, or drugs
• Training, exercise protocols, hypertrophy, strength
• Nutrition, recovery, sleep, circadian biology
• Hormones, endocrinology, TRT
• Dosing, timing, or protocols
• Any mechanism question in biology or physiology