Finish brew updates

Brewfile

@@ -1,4 +1,5 @@
 tap "dart-lang/dart"
+tap "holtwick/tap"
 tap "sass/sass"
 
 brew "ack"
@@ -8,11 +9,11 @@ brew "autoconf"
 brew "automake"
 brew "b2-tools"
 brew "bat"
-brew "bazelisk"
 brew "binwalk"
 brew "cask"
 brew "ccache"
 brew "certbot"
+brew "cloudflared"
 brew "cmake"
 brew "colima"
 brew "devcontainer"
@@ -20,8 +21,11 @@ brew "dfu-util"
 brew "difftastic"
 brew "direnv"
 brew "duck"
+brew "dust"
 brew "earthly"
 brew "esptool"
+brew "fish"
+brew "fq"
 brew "gh"
 brew "ghidra", link: false
 brew "git"
@@ -31,14 +35,18 @@ brew "gnupg"
 brew "go"
 brew "gradle"
 brew "hf"
+brew "holtwick/tap/bx"
 brew "htop"
 brew "httpie"
-brew "huggingface-cli"
 brew "hugo"
 brew "imagemagick"
 brew "john-jumbo"
 brew "jq"
+brew "kubeconform"
+brew "kubectx"
+brew "librsvg"
 brew "lima"
+brew "minikube"
 brew "mise"
 brew "mosh"
 brew "neovim"
@@ -52,6 +60,7 @@ brew "pkgconf"
 brew "protobuf"
 brew "pwgen"
 brew "pwntools"
+brew "python@3.13"
 brew "qemu"
 brew "restic"
 brew "ripgrep"
@@ -93,6 +102,7 @@ cask "rectangle"
 cask "scroll-reverser"
 cask "temurin"
 cask "veracrypt"
+cask "wezterm"
 cask "zulu@17"
 
 def is_corp?
@@ -100,13 +110,22 @@ def is_corp?
   `profiles status -type enrollment 2>/dev/null`.include?("Enrolled via DEP: Yes")
 end
 
+if is_corp?
+  brew "bazelisk", link: false
+end
+
 # non-corp
 if !is_corp?
-  brew "bazel"
+  brew "bazelisk"
   brew "openssh"
+  brew "virt-manager"
+
   cask "claude-code"
   cask "cryptomator"
+  cask "keepassxc"
   cask "gcloud-cli"
   cask "google-cloud-sdk"
+  cask "keybase"
   cask "orbstack"
+  cask "jordanbaird-ice"
 end

bin/macos/update_brewfile

@@ -251,7 +251,13 @@ def main(args):
             if last_type and e.pkg_type != last_type:
                 output_lines.append("")
             last_type = e.pkg_type
-        output_lines.extend(e.to_lines())
+
+        lines = e.to_lines()
+        # If we just added a blank line, and the new lines start with one, skip the first new line
+        if output_lines and output_lines[-1] == "" and lines and lines[0] == "":
+            output_lines.extend(lines[1:])
+        else:
+            output_lines.extend(lines)
 
     new_content = "\n".join(output_lines)
     if footer:

bin/quartz

@@ -0,0 +1,63 @@
+#!/bin/bash
+
+set -euo pipefail
+
+# QUARTZ_DIR search logic
+if [ -z "${QUARTZ_DIR:-}" ]; then
+    if [ -f "quartz.config.ts" ]; then
+        QUARTZ_DIR="$PWD"
+    elif [ -d "$HOME/Personal/notes-quartz" ]; then
+        QUARTZ_DIR="$HOME/Personal/notes-quartz"
+    elif [ -d "$HOME/Projects/notes-quartz" ]; then
+        QUARTZ_DIR="$HOME/Projects/notes-quartz"
+    else
+        echo "Error: QUARTZ_DIR could not be found." >&2
+        exit 1
+    fi
+fi
+
+if [ ! -d "$QUARTZ_DIR" ]; then
+    echo "Error: QUARTZ_DIR '$QUARTZ_DIR' is not a directory." >&2
+    exit 1
+fi
+
+# NOTES_DIR search logic
+PARSE_NOTES_DIR=""
+# Use a copy of args to find -d/--directory
+ARGS=("$@")
+for ((i=0; i<${#ARGS[@]}; i++)); do
+    if [[ "${ARGS[i]}" == "-d" || "${ARGS[i]}" == "--directory" ]]; then
+        if [[ $((i+1)) -lt ${#ARGS[@]} ]]; then
+            PARSE_NOTES_DIR="${ARGS[i+1]}"
+        fi
+        break
+    fi
+done
+
+if [ -n "$PARSE_NOTES_DIR" ]; then
+    NOTES_DIR="$PARSE_NOTES_DIR"
+elif [ -z "${NOTES_DIR:-}" ]; then
+    if [ -d "$HOME/Notes" ]; then
+        NOTES_DIR="$HOME/Notes"
+    elif [ -d "$HOME/Personal/notes" ]; then
+        NOTES_DIR="$HOME/Personal/notes"
+    elif [ -d "$HOME/Projects/notes" ]; then
+        NOTES_DIR="$HOME/Projects/notes"
+    else
+        echo "Error: NOTES_DIR could not be found." >&2
+        exit 1
+    fi
+fi
+
+if [ ! -d "$NOTES_DIR" ]; then
+    echo "Error: NOTES_DIR '$NOTES_DIR' is not a directory." >&2
+    exit 1
+fi
+
+cd "$QUARTZ_DIR"
+
+# Run npx quartz
+# Following the prompt's structure but using NOTES_DIR for the flag
+# npx quartz ${argv[1]} --directory ${NOTES_DIR} "$@"
+# We use ${1:-} for argv[1] to handle cases with no arguments.
+npx quartz "${1:-}" --directory "$NOTES_DIR" "$@"

dotfiles/bxignore

@@ -0,0 +1,4 @@
+# Credentials
+.ssh
+Passwords.kdbx
+Passwords.kdbx.age

dotfiles/config/mise/config.toml

@@ -9,9 +9,8 @@ uv_venv_auto = true
 
 [tools]
 age = "latest"
-age-plugin-yubikey = "latest"
 usage = "latest"
-uv = "latest"
+uv = "0.11.8"
 
 [hooks]
 postinstall = "mise sync python --uv"

dotfiles/gitconfig

@@ -19,14 +19,17 @@
 [difftool]
   prompt = false
 
+[difftool "difftastic"]
+  cmd = difft "$LOCAL" "$REMOTE"
+
 [alias]
   st = status
   last = log -1 HEAD
   # Thanks to
   # http://durdn.com/blog/2012/11/22/must-have-git-aliases-advanced-examples/
-  logs = log --pretty=format:"%C(yellow)%h%Cred%d\\ %Creset%s%Cblue\\ [%cn]" --decorate
+  logs = log --pretty=format:"%C(yellow)%h%Cred%d %Creset%s%Cblue [%cn]" --decorate
   lg = log -p
-  ll = log --pretty=format:"%C(yellow)%h%Cred%d\\ %Creset%s%Cblue\\ [%cn]" --decorate --numstat
+  ll = log --pretty=format:"%C(yellow)%h%Cred%d %Creset%s%Cblue [%cn]" --decorate --numstat
   files = ls-files
   ls = ls-files
   lol = log --graph --pretty=format:'%C(yellow)%h%Creset %an: %s - %Creset %C(yellow)%d%Creset %Cblue(%cr)%Creset' --abbrev-commit --date=relative
@@ -92,8 +95,12 @@
   process = git-lfs filter-process
 
 [include]
+  path = ~/.gitconfig.d/aliases
   path = ~/.gitconfig.d/override
   path = ~/.gitconfig.d/local
 
-[includeIf "gitdir:~/personal/"]
+[includeIf "gitdir/i:~/personal/"]
   path = ~/.gitconfig.d/personal
+
+[rerere]
+  enabled = true

dotfiles/shenv

@@ -15,6 +15,7 @@ export DEBEMAIL="david@systemoverlord.com"
 export DEBFULLNAME="David Tomaschik"
 export LESS="-MR"
 export QUOTING_STYLE="literal"  # Coreutils quotes
+export HOMEBREW_NO_ENV_HINTS=1
 
 # Fix gnome-terminal
 if [ "$TERM" = "xterm" ] && [ "$COLORTERM" = "gnome-terminal" ] ; then

dotfiles/zshrc

@@ -185,6 +185,9 @@ have_command() {
 if test -d ${HOME}/.local/bin ; then
   export PATH="${HOME}/.local/bin:${PATH}"
 fi
+if test -d ${HOME}/.npm-packages/bin ; then
+  export PATH="${HOME}/.npm-packages/bin:${PATH}"
+fi
 
 # Source extras and aliases if interactive
 if [[ $- == *i* ]] ; then

dotfiles/zshrc.d/skelify.zsh

@@ -3,6 +3,17 @@
 # Skelify -- move a file to my .skel and setup symlinks
 
 function skelify {
+  local -A opts
+  zparseopts -D -A opts -overlay:
+
+  local overlay_name="${opts[--overlay]}"
+  local base_skel_dir="${HOME}/.skel/dotfiles"
+  local extra_args=()
+  if [[ -n "${overlay_name}" ]]; then
+    base_skel_dir="${HOME}/.skel/dotfile_overlays/${overlay_name}"
+    extra_args=(--overlay "${overlay_name}")
+  fi
+
   local target
   local whichdir
   local relhome
@@ -10,16 +21,19 @@ function skelify {
   local fulltarget
   for target in $~@; do
     if test -d ${target} ; then
-      skelify ${target}/* || return 1
+      skelify "${extra_args[@]}" ${target}/* || return 1
     elif test -f ${target} ; then
       if ! whichdir=$(cd $(dirname $target) && pwd); then
         echo Could not find directory for $target >/dev/stderr
         return 1
       fi
       fname=$(basename ${target})
-      relhome=${whichdir#${HOME}/}
       fulltarget="${whichdir}/${fname}"
-      if [[ ${relhome} == ${whichdir} ]] ; then
+      if [[ ${whichdir} == ${HOME} ]] ; then
+        relhome=""
+      elif [[ ${whichdir} == ${HOME}/* ]] ; then
+        relhome=${whichdir#${HOME}/}
+      else
         echo ${whichdir} is not in home >/dev/stderr
         return 1
       fi
@@ -32,7 +46,7 @@ function skelify {
         return 1
       fi
       echo ${target}
-      local skeldir="${HOME}/.skel/dotfiles/${relhome}"
+      local skeldir="${base_skel_dir}/${relhome}"
       mkdir -p "${skeldir}"
       mv ${target} "${skeldir}/${fname}"
       ln -s "${skeldir}/${fname}" "${fulltarget}"

dotfiles/zshrc.d/util.zsh

@@ -0,0 +1,56 @@
+# utility function to "open" a file
+o() {
+  if [[ "$OSTYPE" == "darwin"* ]]; then
+    open "$@"
+  elif [[ "$OSTYPE" == "linux-gnu"* ]]; then
+    xdg-open "$@"
+  else
+    echo "Unknown OS"
+  fi
+}
+
+# Copy from stdin to the system clipboard
+syscopy() {
+    if command -v pbcopy >/dev/null 2>&1; then
+        # macOS
+        pbcopy "$@"
+    elif command -v wl-copy >/dev/null 2>&1; then
+        # Linux Wayland
+        wl-copy "$@"
+    elif command -v xclip >/dev/null 2>&1; then
+        # Linux X11
+        xclip -selection clipboard "$@"
+    elif command -v xsel >/dev/null 2>&1; then
+        # Linux X11 (alternative)
+        xsel --clipboard --input "$@"
+    elif command -v clip.exe >/dev/null 2>&1; then
+        # Windows WSL
+        clip.exe "$@"
+    else
+        echo "Error: No clipboard utility found. Please install pbcopy, wl-copy, xclip, or xsel." >&2
+        return 1
+    fi
+}
+
+# Paste from the system clipboard to stdout
+syspaste() {
+    if command -v pbpaste >/dev/null 2>&1; then
+        # macOS
+        pbpaste "$@"
+    elif command -v wl-paste >/dev/null 2>&1; then
+        # Linux Wayland
+        wl-paste "$@"
+    elif command -v xclip >/dev/null 2>&1; then
+        # Linux X11
+        xclip -selection clipboard -o "$@"
+    elif command -v xsel >/dev/null 2>&1; then
+        # Linux X11 (alternative)
+        xsel --clipboard --output "$@"
+    elif command -v powershell.exe >/dev/null 2>&1; then
+        # Windows WSL
+        powershell.exe -noprofile -command Get-Clipboard "$@"
+    else
+        echo "Error: No clipboard utility found. Please install pbpaste, wl-paste, xclip, or xsel." >&2
+        return 1
+    fi
+}