Agent-Skills.md

Agent Skills: bmorphism-ies-env

Documentation and orchestration for the bmorphism/ies flox environment toolkit

UncategorizedID: plurigrid/asi/bmorphism-ies-env

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plurigrid/asi
plurigridLicense: MIT
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skills/bmorphism-ies-env/SKILL.md

Skill Metadata

Name
bmorphism-ies-env
Description
Documentation and orchestration for the bmorphism/ies flox environment toolkit

bmorphism-ies-env

Comprehensive documentation and MCP integration for the 31-tool bmorphism/ies flox environment.

Trit: 0 (ERGODIC) - Infrastructure coordinator Environment: bmorphism/ies Package Count: 31 tools across languages, utilities, and infrastructure

Overview

This skill provides documentation, usage patterns, and MCP tooling for the curated bmorphism/ies flox environment. The environment is optimized for:

  • Multi-language development (Clojure, Julia, Python, Ruby, JavaScript, Java)
  • Systems programming and reverse engineering
  • Data processing and visualization
  • Cloud infrastructure management
  • Text editing and language tooling

Environment Manifest

Programming Languages & Runtimes (8 tools)

babashka (1.12.209)

Purpose: Fast-starting Clojure scripting without JVM overhead Use Cases:

  • Shell scripting with Clojure syntax
  • MCP servers (like flox-mcp-server.bb)
  • Data pipeline orchestration
  • CI/CD scripts

Example:

bb -e "(+ 1 2 3)"  # => 6
bb script.clj      # Run script

Key Features:

  • Instant startup (~10ms)
  • Built-in libraries: cheshire (JSON), babashka.process, babashka.fs
  • Native image compilation via GraalVM
  • SCI (Small Clojure Interpreter) for sandboxing

Documentation: https://book.babashka.org

clojure (1.12.3.1577)

Purpose: Full Clojure runtime with JVM Use Cases:

  • Long-running applications
  • Libraries requiring JVM features
  • Performance-critical code
  • Full ecosystem access

Example:

clj -M -e "(println \"Hello\")"
clj -M:deps tree  # View dependency tree

Documentation: https://clojure.org/guides/getting_started

julia-bin (1.12.3)

Purpose: High-performance scientific computing Use Cases:

  • Numerical analysis
  • Category theory (AlgebraicJulia)
  • DuckDB integration
  • ACSet manipulation

Example:

using Catlab, AlgebraicJulia
# Work with ACSets

Integration: Powers the unworld skill's derivational learning

Documentation: https://docs.julialang.org

nodejs (24.12.0)

Purpose: JavaScript runtime and npm ecosystem Use Cases:

  • Web development
  • CLI tools
  • MCP servers (TypeScript)
  • Build tooling

Example:

node script.js
npm install package
npx create-next-app

Documentation: https://nodejs.org/docs

python312 (3.12.12)

Purpose: General-purpose scripting and data science Use Cases:

  • Data processing (pandas, numpy)
  • Machine learning
  • MCP servers
  • System automation

Example:

python3 -m venv .venv
pip install duckdb pandas

Documentation: https://docs.python.org/3.12/

ruby (3.3.10)

Purpose: Scripting and web development Use Cases:

  • Rails applications
  • DevOps scripts
  • Text processing
  • DSLs

Example:

ruby -e "puts 'Hello'"
gem install bundler

Documentation: https://www.ruby-lang.org/en/documentation/

jdk (21.0.8) / openjdk (21.0.8)

Purpose: Java development and JVM applications Use Cases:

  • Java applications
  • Clojure (full JVM)
  • Scala, Kotlin
  • Enterprise tooling

Example:

javac Program.java
java Program
jshell  # REPL

Documentation: https://docs.oracle.com/en/java/javase/21/

Text Editors & IDEs (2 tools)

emacs (30.2)

Purpose: Extensible, programmable text editor Use Cases:

  • Org-mode literate programming
  • Lisp development
  • Email, RSS, everything
  • MCP integration potential

Key Packages (likely installed):

  • org-mode - Literate programming
  • magit - Git interface
  • lsp-mode - Language servers
  • eshell - Emacs shell

Example:

emacs file.org
emacsclient -c file.jl  # With daemon

Integration: Works with org-babel-execution skill

Documentation: https://www.gnu.org/software/emacs/manual/

helix (25.07.1)

Purpose: Modern modal text editor (Rust-based) Use Cases:

  • Fast file editing
  • Language server protocol (LSP)
  • Multiple selections
  • Terminal-native editing

Example:

hx file.rs
hx --health rust  # Check LSP status

Features:

  • Built-in LSP, DAP, tree-sitter
  • No plugin system needed
  • Multiple cursors
  • Vim-like but different

Documentation: https://docs.helix-editor.com

Developer Tools (5 tools)

gh (2.83.2)

Purpose: GitHub CLI Use Cases:

  • PR management from terminal
  • Issue tracking
  • Repo operations
  • CI/CD inspection

Example:

gh pr create --title "feat: add feature"
gh issue list
gh run watch
gh repo clone user/repo

MCP Integration: Could wrap as MCP tool for AI PR creation

Documentation: https://cli.github.com/manual

graphviz (12.2.1)

Purpose: Graph visualization Use Cases:

  • Dependency diagrams
  • State machines
  • Category theory diagrams
  • Data flow visualization

Example:

dot -Tpng graph.dot -o graph.png
neato -Tsvg network.dot -o network.svg

Integration: Visualize skill dependency graphs, coequalizers

Documentation: https://graphviz.org/documentation/

protobuf (32.1)

Purpose: Protocol Buffers compiler Use Cases:

  • Serialization schemas
  • gRPC services
  • Cross-language data exchange
  • MCP protocol extensions

Example:

protoc --python_out=. schema.proto
protoc --go_out=. service.proto

Documentation: https://protobuf.dev

pkg-config (0.29.2)

Purpose: Library dependency metadata Use Cases:

  • C/C++ compilation
  • Linking system libraries
  • Build system integration

Example:

pkg-config --cflags --libs sqlite3
pkg-config --modversion gtk+-3.0

Documentation: https://www.freedesktop.org/wiki/Software/pkg-config/

tree-sitter (0.25.10)

Purpose: Incremental parsing library Use Cases:

  • Syntax highlighting
  • Code navigation
  • AST analysis
  • Language tooling

Example:

tree-sitter generate
tree-sitter test

Integration: Used by helix, could power code analysis MCP tools

Documentation: https://tree-sitter.github.io/tree-sitter/

Disk Usage Analyzers (4 tools)

dua (2.32.2)

Purpose: Fast disk usage analyzer (Rust) Use Cases:

  • Interactive TUI for disk exploration
  • Fast scanning
  • Deletion from TUI

Example:

dua i          # Interactive mode
dua a /path    # Aggregate view

Comparison: Fastest, interactive, can delete

Documentation: https://github.com/Byron/dua-cli

dust (1.2.3)

Purpose: du + rust = dust (modern du) Use Cases:

  • Tree view of disk usage
  • Colored output
  • Quick overview

Example:

dust           # Current dir
dust -d 3      # Max depth 3
dust -r        # Reverse sort

Comparison: Best for quick visualizations

Documentation: https://github.com/bootandy/dust

gdu (5.32.0)

Purpose: Go-based disk usage analyzer Use Cases:

  • Fast scanning
  • TUI interface
  • Export to JSON

Example:

gdu            # Interactive
gdu -n         # Non-interactive
gdu -o json    # Export format

Comparison: Good balance of speed and features

Documentation: https://github.com/dundee/gdu

ncdu (2.9.2)

Purpose: NCurses disk usage (original) Use Cases:

  • Classic TUI
  • Stable, reliable
  • Scriptable

Example:

ncdu           # Interactive
ncdu -x        # Same filesystem only
ncdu -o file   # Export

Comparison: Most mature, scriptable

Documentation: https://dev.yorhel.nl/ncdu

Recommendation: Use dust for quick checks, dua for interactive exploration

Multimedia & Content (3 tools)

ffmpeg (8.0)

Purpose: Video/audio processing Swiss Army knife Use Cases:

  • Video transcoding
  • Audio extraction
  • Streaming
  • Format conversion

Example:

ffmpeg -i input.mp4 output.webm
ffmpeg -i video.mp4 -vn audio.mp3  # Extract audio
ffmpeg -i input.mp4 -ss 00:01:00 -t 10 clip.mp4  # Clip

Integration: Could power video processing MCP tools

Documentation: https://ffmpeg.org/documentation.html

sox (2021-05-09)

Purpose: Sound eXchange - audio processing Use Cases:

  • Audio effects
  • Format conversion
  • Synthesis
  • Analysis

Example:

sox input.wav output.mp3
sox input.wav output.wav tempo 1.5  # Speed up
play sound.wav  # Play audio

Integration: Sonification of data (catsharp-sonification skill)

Documentation: http://sox.sourceforge.net/sox.html

enchant2 (2.6.9)

Purpose: Spell checking library Use Cases:

  • Text editors
  • Document processing
  • CLI spell check
  • Multiple dictionary support

Example:

enchant-lsmod-2  # List backends
enchant-2 -l file.txt  # Check spelling

Integration: Text validation in documentation skills

Documentation: https://abiword.github.io/enchant/

Infrastructure & Cloud (4 tools)

google-cloud-sdk (548.0.0)

Purpose: Google Cloud Platform CLI Use Cases:

  • GCP resource management
  • Cloud Storage
  • BigQuery
  • Kubernetes (GKE)

Example:

gcloud auth login
gcloud compute instances list
gsutil cp file.txt gs://bucket/
bq query "SELECT * FROM dataset.table LIMIT 10"

MCP Integration: Wrap GCP operations as MCP tools

Documentation: https://cloud.google.com/sdk/docs

nats-server (2.12.3)

Purpose: NATS message broker Use Cases:

  • Pub/sub messaging
  • Service mesh
  • Event streaming
  • MCP transport layer

Example:

nats-server                    # Start server
nats-server -js                # With JetStream
nats-server -c nats-server.conf  # Config file

Integration: Could power distributed MCP server communication

Documentation: https://docs.nats.io

tailscale (1.92.3)

Purpose: Mesh VPN (WireGuard-based) Use Cases:

  • Secure remote access
  • Service networking
  • Exit nodes
  • MagicDNS

Example:

tailscale up
tailscale status
tailscale ip -4
tailscale serve 8080  # Expose service

Integration: Secure MCP server networking (tailscale-localsend skill)

Documentation: https://tailscale.com/kb/

wash-cli (1.0.0-beta.10)

Purpose: WebAssembly Shell (wasmCloud CLI) Use Cases:

  • WebAssembly component management
  • wasmCloud orchestration
  • WASI development
  • Distributed apps

Example:

wash up          # Start wasmCloud host
wash ctl get hosts
wash build       # Build component
wash app deploy app.yaml

Integration: Deploy MCP servers as Wasm components

Documentation: https://wasmcloud.com/docs/cli

System Utilities (3 tools)

coreutils (9.8)

Purpose: GNU core utilities Use Cases:

  • Basic file operations (ls, cp, mv, rm)
  • Text processing (cat, cut, sort, uniq)
  • System info (whoami, hostname, uptime)

Example:

ls -lah
cat file.txt | sort | uniq -c
seq 1 10 | xargs -I{} echo "Item {}"

Note: macOS ships with BSD utilities; this provides GNU versions

Documentation: https://www.gnu.org/software/coreutils/manual/

nickel (1.15.1)

Purpose: Configuration language Use Cases:

  • Type-safe configs
  • Contract validation
  • Nix integration
  • Infrastructure as code

Example:

nickel export config.ncl --format json
nickel query config.ncl
nickel repl

Integration: The asi repo has 440 .ncl files - skill configurations!

ASI Integration:

ls skills/**/*.ncl | wc -l  # 440 Nickel files

Documentation: https://nickel-lang.org

Verification & Security (2 tools)

dafny (4.11.0)

Purpose: Verification-aware programming language Use Cases:

  • Formal verification
  • Proof-carrying code
  • Algorithm correctness
  • Secure protocol design

Example:

dafny verify program.dfy
dafny /compile:3 program.dfy  # Compile to C#
dafny format file.dfy

Integration: Could verify GF(3) conservation proofs formally

Documentation: https://dafny.org/latest/OnlineTutorial/guide

radare2 (6.0.7)

Purpose: Reverse engineering framework Use Cases:

  • Binary analysis
  • Debugging
  • Disassembly
  • Exploit development (authorized contexts)

Example:

r2 binary
r2 -A binary      # Analyze all
rabin2 -I binary  # Binary info
rasm2 "mov eax, 33"  # Assemble

Security Note: Only use for authorized security testing, CTFs, research

Documentation: https://r2wiki.readthedocs.io

Python Tooling (1 tool)

uv (0.9.21)

Purpose: Extremely fast Python package installer (Rust) Use Cases:

  • pip replacement (10-100x faster)
  • Virtual environment management
  • Dependency resolution
  • Lock file generation

Example:

uv pip install pandas numpy
uv venv .venv
uv pip compile requirements.in  # Generate lock
uv pip sync requirements.txt    # Sync to lock

Performance: ~100x faster than pip for cold installs

Documentation: https://github.com/astral-sh/uv

MCP Integration Patterns

Pattern 1: Direct CLI Wrapping

;; flox-mcp-server.bb pattern
(defn run-tool [tool & args]
  (let [result (p/shell {:out :string :err :string :continue true}
                        (str/join " " (cons tool args)))]
    {:exit (:exit result)
     :stdout (str/trim (:out result))
     :stderr (str/trim (:err result))}))

;; Example: Wrap gh CLI
(defn handle-gh-pr-create [{:keys [title body]}]
  (run-tool "gh" "pr" "create" "--title" title "--body" body))

Pattern 2: Batch Operations

;; Run multiple tools in sequence
(defn analyze-repo [repo-path]
  (let [disk-usage (run-tool "dust" repo-path)
        git-status (run-tool "gh" "repo" "view")
        tree-check (run-tool "tree-sitter" "test")]
    {:disk disk-usage
     :git git-status
     :syntax tree-check}))

Pattern 3: Streaming Output

;; Stream ffmpeg progress
(defn stream-transcode [input output]
  (let [proc (p/process ["ffmpeg" "-i" input output] 
                        {:inherit true})]
    ;; Send progress notifications via MCP
    ))

GF(3) Triad Examples

Triad 1: Language Ecosystem

julia-bin (+1, PLUS)      # Generative (AlgebraicJulia)
babashka (0, ERGODIC)     # Coordinator (MCP servers)
dafny (-1, MINUS)         # Validator (formal verification)

Sum: +1 + 0 + (-1) ≡ 0 (mod 3) ✓

Triad 2: Disk Analysis

dust (+1, PLUS)           # Quick generation of views
gdu (0, ERGODIC)          # Balanced analysis
ncdu (-1, MINUS)          # Deep validation

Triad 3: Cloud Infrastructure

wash-cli (+1, PLUS)       # Deploy new components
tailscale (0, ERGODIC)    # Network coordination
google-cloud-sdk (-1, MINUS)  # Validate resources

Tool Selection Guide

Use Case: Quick Script

Choose: babashka or python312

  • Babashka: If Clojure familiarity, need speed
  • Python: If data processing, ML, broader ecosystem

Use Case: Scientific Computing

Choose: julia-bin

  • Best for: Numerical analysis, category theory, performance
  • Integration: AlgebraicJulia, DuckDB.jl

Use Case: Disk Space Cleanup

Choose: dua (interactive) or dust (quick view)

  • dua: When you want to delete files interactively
  • dust: When you just need a quick tree view

Use Case: Video Processing

Choose: ffmpeg

  • No alternatives needed - it's the standard

Use Case: Text Editing

Choose: helix (fast, terminal) or emacs (powerful, GUI)

  • helix: Quick edits, LSP integration, modern UX
  • emacs: Org-mode, extensive customization, Lisp

Use Case: Reverse Engineering

Choose: radare2

  • Comprehensive framework for binary analysis
  • Use only in authorized contexts

Environment Updates

Check for Updates

flox list | grep "upgrade available"

Current outdated packages:

  • dua: 2.32.2 → newer available
  • tailscale: 1.92.3 → newer available
  • uv: 0.9.21 → newer available

Upgrade Packages

flox upgrade dua tailscale uv

Add New Tools

flox search ripgrep
flox install ripgrep

Remove Tools

flox uninstall package-name

Integration with Other Skills

Skills Using These Tools

  • flox-mcp - Wraps flox CLI for environment management
  • org-babel-execution - Uses emacs org-mode
  • unworld - Julia-based derivational learning
  • catsharp-sonification - sox for audio synthesis
  • babashka-clj - Babashka scripting patterns
  • gay-mcp - Could use dafny for GF(3) verification
  • tailscale-localsend - Tailscale mesh networking
  • nickel skill (440 .ncl files in asi repo)

Potential New Skills

  1. gh-mcp - GitHub CLI wrapper for AI PR management
  2. ffmpeg-pipeline - Video processing orchestration
  3. dafny-verifier - Formal verification of GF(3) properties
  4. radare2-analyzer - Binary analysis (security research only)
  5. nats-broker - Message broker for distributed MCP
  6. tree-sitter-parser - Code analysis and navigation

Environment Statistics

Total Packages: 31
Languages: 8 (Clojure, Julia, JS, Python, Ruby, Java)
Editors: 2 (emacs, helix)
Disk Analyzers: 4 (dua, dust, gdu, ncdu)
Cloud Tools: 4 (gcloud, nats, tailscale, wash)
Security/Verification: 2 (dafny, radare2)
Multimedia: 3 (ffmpeg, sox, enchant2)

Total Install Size: ~5GB
Active Environment: bmorphism/ies
FloxHub: hub.flox.dev/bmorphism/ies

Skill Name: bmorphism-ies-env Type: Environment Documentation & MCP Integration Trit: 0 (ERGODIC - Infrastructure Coordinator) Status: ✅ Production (31 tools documented)