chore: consolidate dotfiles and add AI agent configs

[kylejb]

No description provided.

[Copilot]

Pull request overview

This PR modernizes the dotfiles “script architecture” around POSIX sh entrypoints (self-contained DOTFILES + utils.sh sourcing), adds machine profiles (personal vs work) for gating behavior, and introduces shareable AI agent configuration management (Claude + Codex) applied via dot --apply.

Changes:

• Add standardized OS detection + machine profile helpers in utils.sh and export DOTFILES_PROFILE early from zshenv.
• Expand dot CLI and scripts to support --apply, --defaults, and --uninstall, and split “install tools” vs “apply config”.
• Add AI agent config syncing (symlinks + Codex config fragment merge) and gitignore rules to avoid syncing runtime/secret state.

Reviewed changes

Copilot reviewed 27 out of 31 changed files in this pull request and generated 14 comments.

Show a summary per file

File	Description
zsh/zshenv.symlink	Exports DOTFILES_PROFILE early from an XDG config file for consistent gating across shell/topics.
vscode/install.sh	Starts using utils.sh OS predicates; manages VS Code settings symlinks/extensions.
uv/update.sh	Switches to sh shebang for portability.
uv/install.sh	Switches to sh + set -e; sources utils.sh.
utils.sh	Adds POSIX-friendly OS detection helpers + machine profile helpers; refines formatting helpers.
ssh/apply.sh	Converts to sh, uses OS predicates, ensures ~/.ssh exists before linking config.
script/vscode-extensions	Removed legacy VS Code extension installer script.
script/update	Self-contained update runner; gates macOS-only system updates and runs all update.sh.
script/uninstall	New script to remove dotfile symlinks that point into $DOTFILES.
script/post-bootstrap	Removed legacy post-bootstrap orchestration script.
script/install	Shebang updated to sh (installer runner remains as-is).
script/bootstrap	Refactors bootstrap flow: base dirs, profile setup, OS-aware tool installs, apply step, macOS defaults.
script/apply	New “config-only” path to create symlinks and run all */apply.sh renderers/linkers.
mise/update.sh	Switches to sh shebang for portability.
mise/install.sh	Switches to sh + set -e; uses OS predicates; tightens curl flags.
macos/set-defaults.sh	Fixes utils.sh sourcing path and shellcheck directives.
linux/install.sh	Updates shellcheck directives for utils.sh sourcing.
linux/debian.sh	Replaces which with command -v for POSIX portability.
gnupg/apply.sh	Uses OS predicates; updates error message to uname-based platform string.
dotfiles.sh	Removes unused/legacy entrypoint script.
codespaces/installer.sh	Switches to sh, improves robustness of shell env steps (e.g., rm -f, command -v).
bin/dot	Expands CLI flags (--apply, --defaults, --uninstall) and adds Windows guard.
ai/codex/README.md	Documents Codex config structure and the managed-block merge approach for config.toml.
ai/codex/prompts/.gitkeep	Adds placeholder for shareable Codex prompts directory.
ai/codex/config.d/mcp.toml.example	Example MCP server fragment templates (committed vs local secret-bearing).
ai/codex/config.d/.gitkeep	Adds placeholder for Codex config fragments directory.
ai/claude/settings.json	Adds shareable Claude settings.
ai/claude/CLAUDE.md	Adds shared, tool-agnostic agent standards (symlinked into Claude + Codex).
ai/apply.sh	New AI config applier: symlinks trees and merges Codex fragments into managed block.
.gitignore	Adds macOS .DS_Store ignores and AI runtime/secret-state ignores; ignores local Codex fragments.
.github/README.md	Documents new dot workflow, machine profiles, and self-contained script architecture.

Comments suppressed due to low confidence (7)

vscode/install.sh:29

• On macOS the symlink destination is hard-coded to .../settings.json, so if more files are added (keybindings/snippets) the loop would overwrite the same destination repeatedly. Use the per-file destination directory and link to $file (and create the directory first).

    if is_macos; then
        ln -svf "${DOTFILES}/vscode/$file" "$HOME/Library/Application Support/Code/User/settings.json"
    elif is_linux; then
        ln -svf "${DOTFILES}/vscode/$file" "$HOME/.config/Code/User/$file"
    else
        echo 'Unsupported OS detected. Skipping VSCode setup...'
    fi

mise/install.sh:18

• After a fresh install, the script exits early (exit 0) and never runs the rest of the setup (completion + tool installs). Also command -v is being used with a file path, which is not a valid way to check/install mise in POSIX sh.

  if command -v "${HOME}/.local/bin/mise"; then
    echo 'Successfully installed mise'
    exit 0
  fi
  echo 'Unable to locate mise after installation' 1>&2
  exit 1

gnupg/apply.sh:4

• This script sources ${DOTFILES}/utils.sh but does not set a fallback for DOTFILES, so it will fail when invoked standalone.
  gnupg/apply.sh:11
• Likely typo: pinentry-curse doesn’t match the common binary name (pinentry-curses) and contradicts the comment below. As written, this will point GnuPG at a non-existent pinentry on most Linux installs.
  ssh/apply.sh:4
• ssh/apply.sh sources ${DOTFILES}/utils.sh but never sets a default for DOTFILES, so it will fail when invoked standalone (and script/apply runs appliers via sh, so they should be self-contained).
  ssh/apply.sh:18
• echo in POSIX sh does not reliably interpret \n, so the Include ...\n line is likely to be written with a literal \n in the ssh config. Use printf to emit a real newline.
  ssh/apply.sh:21
• Same echo/newline issue for the macOS include line — \n may be literal in many sh implementations. Prefer printf for predictable output.

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[Copilot]

Pull request overview

Copilot reviewed 27 out of 31 changed files in this pull request and generated 6 comments.

Comments suppressed due to low confidence (6)

script/install:6

• This runner script uses $DOTFILES without ensuring it is set, and uses sh -c to run the installer path as a string. Per the repo’s “self-contained scripts” convention, it should set DOTFILES, source utils.sh, and execute installers via sh "$installer".

#!/bin/sh
# Run all dotfiles installers.

set -e

find "${DOTFILES}" -name install.sh | while read -r installer; do sh -c "${installer}"; done

ssh/apply.sh:20

• This echo writes a literal \n into the ssh config (single quotes prevent escape expansion), which will break the Include directive. It also writes tmp_config into the current working directory. Use printf for the newline and write the temp file under src_dir.
  ssh/apply.sh:23
• Same issue as the Linux branch above: this writes a literal \n and uses a temp file in the current working directory. Use printf and keep the temp file under src_dir.
  script/install:6
• This runner script uses $DOTFILES without ensuring it is set, and uses sh -c to run the installer path as a string. Per the repo’s “self-contained scripts” convention, it should set DOTFILES, source utils.sh, and execute installers via sh "$installer".

#!/bin/sh
# Run all dotfiles installers.

set -e

find "${DOTFILES}" -name install.sh | while read -r installer; do sh -c "${installer}"; done

ssh/apply.sh:20

• This echo writes a literal \n into the ssh config (single quotes prevent escape expansion), which will break the Include directive. It also writes tmp_config into the current working directory. Use printf for the newline and write the temp file under src_dir.
  ssh/apply.sh:23
• Same issue as the Linux branch above: this writes a literal \n and uses a temp file in the current working directory. Use printf and keep the temp file under src_dir.

[Copilot]

Pull request overview

Copilot reviewed 27 out of 31 changed files in this pull request and generated 5 comments.

Comments suppressed due to low confidence (3)

script/install:6

• script/install isn't self-contained (it assumes $DOTFILES is already set) and it runs installers via sh -c, which is unsafe (word-splitting) and also ignores shebang options like #!/bin/sh -e. This breaks running the script standalone and can hide failures in installers that rely on -e.

set -e

find "${DOTFILES}" -name install.sh | while read -r installer; do sh -c "${installer}"; done

uv/install.sh:12

• uv/install.sh relies on command_exists uv/uv ..., but bootstrap runs in a non-interactive shell where ~/.local/bin typically is NOT on $PATH. This can cause false negatives (reinstall loops) or failures right after install. Add ~/.local/bin to PATH for the duration of the script.

# shellcheck disable=SC3046 source=/dev/null
. "${DOTFILES}/utils.sh"

if ! command_exists uv; then
  echo 'Installing uv'
  curl -LsSf https://astral.sh/uv/install.sh | sh
  command_exists uv || { echo 'Unable to locate uv after installation' 1>&2; exit 1; }

vscode/install.sh:46

• Even when $code_user is empty (unsupported OS) or the code CLI isn't on PATH, the script still calls install_extensions, which will fail under #!/bin/sh -e. Gate extension installation on both a supported OS and command_exists code.

if [ -n "$code_user" ]; then
    mkdir -p "$code_user"
    # Link each tracked config file to its OWN destination (not all to settings.json).
    for name in settings.json keybindings.json; do
        src="${DOTFILES}/vscode/$name"
        [ -e "$src" ] && ln -sfnv "$src" "$code_user/$name"
    done
    # Snippets directory, if present.
    [ -d "${DOTFILES}/vscode/snippets" ] && ln -sfnv "${DOTFILES}/vscode/snippets" "$code_user/snippets"
fi

install_extensions