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jstack is a single repository that owns every tracked file under ~/.claude/. Three concerns are kept separate: layout (what files exist in the repo), install (how they reach ~/.claude/), and runtime (what binaries Claude Code can call).

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Layout

.
├── settings.json              # source of truth for ~/.claude/settings.json
├── CLAUDE.md                  # source of truth for ~/.claude/CLAUDE.md
├── skills/                    # personal skills (dir-per-skill, SKILL.md inside)
├── agents/                    # personal subagent .md files
├── commands/                  # personal slash command .md files
├── hooks/                     # hook scripts referenced from settings.json
├── plugins/                   # one directory per plugin bundle
├── runtime/default.nix        # pkgs.buildEnv with MCP servers, LSPs
├── evals/                     # promptfoo eval suite
└── scripts/
    ├── install.bash           # link the repo into ~/.claude, build runtime
    └── eval.bash              # run promptfoo (--fast for routing only)

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Install model

scripts/install.bash is a symlink installer. For each tracked top-level file or directory, it:
  1. Refuses to run as root.
  2. Verifies the repo looks like a jstack checkout (settings.json and skills/ must exist).
  3. Symlinks settings.json and CLAUDE.md into ~/.claude/.
  4. Symlinks skills/, agents/, commands/, hooks/, and plugins/ into ~/.claude/.
  5. Builds the runtime via nix-build runtime/default.nix and links the result under ~/.local/state/jstack/runtime.
  6. Updates the shell rc so ~/.local/state/jstack/runtime/bin is on PATH.
Anything the installer would displace is moved into a timestamped backup under ~/.claude/.jstack-backups/<timestamp>/. A RESTORE.md is dropped alongside. The installer is idempotent: re-running on a clean tree reports zero actions.

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Runtime model

runtime/default.nix is a pkgs.buildEnv derivation. Whatever binaries it includes are exposed to Claude Code via PATH. The current build includes:
  • pyright — Python LSP
  • nil — Nix LSP
  • typescript-language-server — TS/JS LSP
Additional MCP servers and LSPs go in the same paths list. After editing runtime/default.nix, re-run install.bash to rebuild and re-link.

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Plugins

Each plugin lives at plugins/<name>/ and is self-contained. The expected layout per plugin: 
plugins/<name>/
├── .claude-plugin/plugin.json   # required: name, description, author
├── README.md                    # what it ships, sources, license
├── .mcp.json                    # optional: MCP server wiring
└── skills/
    └── <skill-name>/SKILL.md
install.bash symlinks the entire plugins/ tree as a single unit, so new plugins are picked up without touching the installer.

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Marketplace UI conflict

After install, ~/.claude/plugins/ is a symlink into this repo. If you install a plugin via Claude Code’s marketplace UI (/plugin install foo), it writes a new directory under plugins/ and shows up in git status. Either commit the new plugin to the repo or revert it.

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Why no submodules

An earlier iteration of jstack vendored upstream plugin sources via git submodules under vendor/, with symlinks into plugins/jstack-vendored/. That layer was removed: every plugin currently shipped is owned content that lives directly under plugins/<name>/. There is no vendor/ and no bump-vendor.bash.
Last modified on April 8, 2026