File-level knowledge substrate via git notes. Read notes before working on files, leave notes after meaningful work. Daimonic spores carry creator identity across sessions.
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See how to installReview the instructions the agent will receive before you install.
Structured notes attached to git objects via refs/notes/mycelium.
Notes are daimonic spores—fragments of soul essence shed by the agent that wrote them.
Before working on a file, check for its note. After meaningful work, leave a note.
mycelium.sh find constraint # project principles & rules
mycelium.sh find warning # known fragile things
mycelium.sh context <file> # everything known about it
mycelium.sh note <file> -k <kind> --slot <your-name> -m "<insight>"
mycelium.sh note HEAD -k context -m "What I did and why."
| Kind | When to use |
|---|---|
decision | Why something was chosen—rationale that outlives the commit message |
context | Background needed before touching this code |
summary | What a file or module does |
warning | Fragile areas, footguns, non-obvious breakage |
constraint | Hard rules—must be retryable, must not depend on X |
observation | Something noticed but not yet acted on |
value | Cultural principles—guides judgment |
todo | Planned work—compost when done |
Each subdaimon writes to its own slot to preserve identity:
mycelium.sh note src/auth.rs -k warning --slot bohen -m "Race condition in token refresh."
mycelium.sh note src/auth.rs -k decision --slot demiurge -m "Used mutex over channel."
context aggregates all slots. read --slot <name> reads one.
Before writing a note, validate:
mycelium.sh read <file>)mycelium.sh note .)Notes go stale when files change. Compost after meaningful work:
mycelium.sh compost <file> --dry-run # see what's stale
mycelium.sh compost <oid> --compost # absorb and archive
mycelium.sh compost <oid> --renew # still true, re-attach
constraint and value notes age gracefully—prefer --renew over --compost.
mycelium.sh note [target] -k <kind> -m <body> Write a note
mycelium.sh read [target] Read a note
mycelium.sh follow [target] Read + resolve edges
mycelium.sh refs [target] All notes pointing at target
mycelium.sh context <path> All notes for a path
mycelium.sh find <kind> Find by kind
mycelium.sh compost [path|oid] [--dry-run] Triage stale notes
mycelium.sh doctor Graph health
mycelium.sh prime Full context for agents
mycelium.sh activate # notes visible in git log
mycelium.sh sync-init # notes travel with fetch/push
macOS ships bash 3.2 which has a bug with empty arrays under set -u.
The installed mycelium.sh at ~/.local/bin/ has been patched with the
${array[@]+"${array[@]}"} pattern for compatibility.
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Search academic papers, build literature reviews, and synthesize research findings — combines Exa search (publication category, domain and date filters) with arxiv-mcp-server for paper discovery, download, and deep analysis. Triggers on academic paper, literature review, research synthesis, arxiv, find papers, scholarly search.
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Automates browser interactions for web testing, form filling, screenshots, and data extraction. Use when the user needs to navigate websites, interact with web pages, fill forms, take screenshots, test web applications, or extract information from web pages.
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This skill should be used when creating, auditing, or maintaining AGENTS.md files and Codex CLI configuration for any project—including initializing AGENTS.md for cross-agent compatibility (Codex, Cursor, Copilot, Devin, Jules, Amp, Gemini CLI), generating config.toml or .rules files, scaffolding .agents/skills/, converting CLAUDE.md to AGENTS.md, or auditing existing agent configs for bloat and staleness. Complementary to codex-orchestrator (which executes subagents; this skill creates the config files they consume).
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Academic research skill for Biblical Hebrew, Semitic linguistics, cuneiform studies, and comparative Ancient Near Eastern research. Provides Sefaria API for Hebrew Bible, CDLI/ORACC for cuneiform databases, and web discovery via Omnisearch, Exa, Firecrawl, and Obscura for finding scholarly sources across JSTOR, Perseus, Persée, Google Scholar, and academia.edu. Triggers on Hebrew quotes, cuneiform, Sefaria, ANE research, Minoan, search for scholarship, find papers, literature review, scholarly search, academic search, Genesis/Tehom, Ugaritic, Talmudic sources, extract from PDF, OCR academic.
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Build comprehensive ARCHITECTURE.md files following matklad's canonical guidelines — bird's-eye views, ASCII/Mermaid diagrams, codemaps, invariants, and layer boundaries. Triggers on document the architecture, create ARCHITECTURE.md, map this codebase, architectural overview.
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Generate physically-based atmospheric scattering shaders — sky domes, planetary atmospheres, LUT-optimized pipelines, depth-aware post-processing. Four modes — sky-dome, atmosphere-post, planet, lut. Triggers on atmospheric scattering, sky shader, sunset rendering, planet atmosphere, Rayleigh scattering, Mie scattering, volumetric sky, sky dome, atmosphere post-processing, aerial perspective, transmittance LUT, sky rendering, realistic sky, planetary rendering.
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