Fix non-idiomatic config and bugs found during dotfiles review

ansible/tasks/link_files.yml

@@ -18,7 +18,7 @@
     - { src: "fish/fish_plugins", dest: ".config/fish/fish_plugins" }
     - {
         src: "fish/completions/fish_gh_completion.fish",
-        dest: ".config/fish/fish_gh_completion",
+        dest: ".config/fish/completions/fish_gh_completion.fish",
       }
     - { src: "atuin/config.toml", dest: ".config/atuin/config.toml" }
     - { src: "lazygit/config.yml", dest: ".config/lazygit/config.yml" }
@@ -28,7 +28,6 @@
     # Scripts for working with data
     - { src: "parquet/csv_to_parquet.py", dest: ".bin/csv_to_parquet" }
     - { src: "parquet/parquet_to_csv.py", dest: ".bin/parquet_to_csv" }
-    - { src: "yml/format_yml.py", dest: ".bin/format_yml" }
 
     # Misc. scripts and config
     - { src: "zettel/today.sh", dest: ".bin/today" }

ansible/tasks/neovim.yml

@@ -13,7 +13,6 @@
       - pynvim
       - pyright
       - ruff
-      - ruff-lsp
       - yamllint
 
 - name: Remove existing ftplugin directory if it exists (to allow symlinking)

bash/bashrc

@@ -88,50 +88,52 @@ export GIT_COMMITTER_EMAIL=$EMAIL
 export PAGER='less'
 export LESS='-R -M --shift 5'
 
-export JAVA_HOME=$(/usr/libexec/java_home -v 18)
+# Java home (only set if java_home exists and returns a valid path)
+if [ -x /usr/libexec/java_home ]; then
+    _java_home=$(/usr/libexec/java_home 2>/dev/null)
+    if [ -n "$_java_home" ]; then
+        export JAVA_HOME="$_java_home"
+    fi
+    unset _java_home
+fi
 
 # language
 export LC_ALL='en_GB.UTF-8'
 export LANG='en_GB.UTF-8'
-export LC_CTYPE=C
-export DISPLAY=:0
 
 ###################################################################
 #
-# Shell history improvements
+# Bash-specific settings (skipped when sourced from zsh)
 #
 ###################################################################
 
-export HISTSIZE=50000
-export HISTFILESIZE=100000
-export HISTCONTROL=ignoredups:erasedups
-export HISTTIMEFORMAT="[%F %T] "
-shopt -s histappend  # Append to history, don't overwrite
-
-###################################################################
-#
-# Modern shell tool initialization
-#
-###################################################################
-
-# Initialize starship prompt
-if command -v starship &>/dev/null; then
-    eval "$(starship init bash)"
-fi
-
-# Initialize zoxide for smart directory navigation
-if command -v zoxide &>/dev/null; then
-    eval "$(zoxide init bash)"
-fi
-
-# Initialize atuin for enhanced shell history
-if command -v atuin &>/dev/null; then
-    eval "$(atuin init bash)"
-fi
-
-# Initialize mise for runtime version management
-if command -v mise &>/dev/null; then
-    eval "$(mise activate bash)"
+if [ -n "$BASH_VERSION" ]; then
+    # Shell history improvements
+    export HISTSIZE=50000
+    export HISTFILESIZE=100000
+    export HISTCONTROL=ignoredups:erasedups
+    export HISTTIMEFORMAT="[%F %T] "
+    shopt -s histappend  # Append to history, don't overwrite
+
+    # Initialize starship prompt
+    if command -v starship &>/dev/null; then
+        eval "$(starship init bash)"
+    fi
+
+    # Initialize zoxide for smart directory navigation
+    if command -v zoxide &>/dev/null; then
+        eval "$(zoxide init bash)"
+    fi
+
+    # Initialize atuin for enhanced shell history
+    if command -v atuin &>/dev/null; then
+        eval "$(atuin init bash)"
+    fi
+
+    # Initialize mise for runtime version management
+    if command -v mise &>/dev/null; then
+        eval "$(mise activate bash)"
+    fi
 fi
 
 
@@ -145,27 +147,26 @@ fi
 # For full GNU environment, add to PATH instead:
 # export PATH="$(brew --prefix)/opt/coreutils/libexec/gnubin:$PATH"
 
-if command -v brew >/dev/null 2>&1; then
-    brew_prefix=$(brew --prefix)
-
+# Check for coreutils by looking for a binary instead of running brew --prefix
+if [ -x /opt/homebrew/bin/gcat ]; then
+    brew_prefix=/opt/homebrew
+
     # Core file operations
     alias cp="$brew_prefix/bin/gcp"
     alias mv="$brew_prefix/bin/gmv"
     alias rm="$brew_prefix/bin/grm"
-    
+
     # Text processing
     alias sed="$brew_prefix/bin/gsed"
     alias awk="$brew_prefix/bin/gawk"
     alias grep="$brew_prefix/bin/ggrep"
-    
+
     # Date/time
     alias date="$brew_prefix/bin/gdate"
-    
+
     # System info
     alias stat="$brew_prefix/bin/gstat"
     alias readlink="$brew_prefix/bin/greadlink"
-
-    # Note: ls/cat/find are overridden with modern alternatives (eza/bat/fd) in aliases section above
 fi
 
 # Source local overrides if they exist

fish/config.fish

@@ -1,5 +1,3 @@
-#!/usr/local/bin/fish
-
 # --- XDG Base Directory Specification ---
 set -x XDG_CONFIG_HOME $HOME/.config
 set -x XDG_DATA_HOME $HOME/.local/share
@@ -88,6 +86,7 @@ fish_add_path $HOMEBREW_BIN
 fish_add_path $DOTFILES_BIN
 fish_add_path $USER_BIN
 fish_add_path $LOCAL_BIN
+fish_add_path $PYTHON_BIN
 
 # FZF configuration with better preview
 set -x FZF_DEFAULT_COMMAND 'fd --type f --hidden --follow --exclude .git'
@@ -110,16 +109,17 @@ set -x GIT_COMMITTER_EMAIL $EMAIL
 set -x PAGER less
 set -x LESS '-R -M --shift 5'
 
-# Java home - commented out as it adds startup delay
-# if test -x /usr/libexec/java_home
-#     set -x JAVA_HOME (/usr/libexec/java_home -v 18 2>/dev/null)
-# end
+# Java home (only set if java_home exists and returns a valid path)
+if test -x /usr/libexec/java_home
+    set -l java_home (/usr/libexec/java_home 2>/dev/null)
+    if test -n "$java_home"
+        set -gx JAVA_HOME $java_home
+    end
+end
 
 # Language settings
 set -x LC_ALL 'en_GB.UTF-8'
 set -x LANG 'en_GB.UTF-8'
-set -x LC_CTYPE C
-set -x DISPLAY :0
 
 ###################################################################
 #
@@ -151,9 +151,9 @@ end
 #
 ###################################################################
 
-# Improve the ssh function to use mosh only when appropriate
+# Use mosh when connecting to a simple hostname with no extra arguments
 function ssh
-    if test (count $argv) -gt 0; and string match -qr '^[a-zA-Z0-9._-]+$' -- $argv[1]
+    if test (count $argv) -eq 1; and string match -qr '^[a-zA-Z0-9._-]+$' -- $argv[1]
         mosh $argv
     else
         command ssh $argv
@@ -166,7 +166,7 @@ end
 
 # Cat the contents of a file into the clipboard
 function pbcat
-    cat $argv[1] | pbcopy
+    command cat $argv[1] | pbcopy
 end
 
 # Use ctrl+s to fzf search the current directory
@@ -182,21 +182,19 @@ bind \cg wiki_file
 
 # Search for all files *containing* text
 function wt
-    set dir (pwd)
-    cd ~/Dropbox/wiki/zettel/; and rg $argv[1] --files-with-matches \
-        | fzf --preview 'bat --style=numbers --color=always {}' --preview-window="right:65%" --height="70%" \
-        | xargs -I {} -o nvim ~/Dropbox/wiki/zettel/{}
-    cd $dir
+    rg $argv[1] --files-with-matches ~/Dropbox/wiki/zettel/ \
+        | fzf --preview "bat --style=numbers --color=always {}" --preview-window="right:65%" --height="70%" \
+        | xargs -I {} -o nvim {}
 end
 
 # LESS colors for man pages
-set -Ux LESS_TERMCAP_us \e\[1\;32m
-set -Ux LESS_TERMCAP_md \e\[1\;31m
-set -Ux LESS_TERMCAP_mb \e\[01\;31m
-set -Ux LESS_TERMCAP_me \e\[0m
-set -Ux LESS_TERMCAP_se \e\[0m
-set -Ux LESS_TERMCAP_so \e\[01\;44\;33m
-set -Ux LESS_TERMCAP_ue \e\[0m
+set -gx LESS_TERMCAP_us \e\[1\;32m
+set -gx LESS_TERMCAP_md \e\[1\;31m
+set -gx LESS_TERMCAP_mb \e\[01\;31m
+set -gx LESS_TERMCAP_me \e\[0m
+set -gx LESS_TERMCAP_se \e\[0m
+set -gx LESS_TERMCAP_so \e\[01\;44\;33m
+set -gx LESS_TERMCAP_ue \e\[0m
 
 # Source local environment variables if they exist
 if test -f ~/.local/environment.fish

git/clean_branches.sh

@@ -1,48 +1,48 @@
 #!/bin/bash
 #
-# Remove any local branches that don't exist on the origin
+# Remove local branches that have been merged and no longer exist on the remote.
+# Protects main, master, and the currently checked-out branch.
 #
+# Usage: clean_branches.sh [-f]
+#   -f  Force delete unmerged branches that no longer exist on remote
 
 set -o errexit
+set -o nounset
 
-#!/bin/bash
-
-# Check if Git is installed
-if ! git --version >/dev/null 2>&1; then
-  echo "Error: Git is not installed. Please install Git and try again."
-  exit 1
-fi
-
-# Check if the current directory is a Git repository
 if ! git rev-parse --is-inside-work-tree >/dev/null 2>&1; then
-  echo "Error: The current directory is not a Git repository. Please navigate to a Git repository and try again."
+  echo "Error: not inside a git repository."
   exit 1
 fi
 
-# Check for the -f flag
 force_delete=false
-if [[ "$1" == "-f" ]]; then
+if [[ "${1:-}" == "-f" ]]; then
   force_delete=true
 fi
 
-# Fetch the latest changes from the remote repository and prune deleted branches
+# Fetch and prune remote tracking branches
 git fetch --prune
 
-# Get a list of merged branches and filter out the branches that no longer exist on the origin
-merged_branches=$(git branch --merged | grep -v "\*" | grep -v "^\s*master" | grep -v "^\s*main" | xargs -n 1 git branch -r --contains | sed 's/origin\///' | uniq)
+current_branch=$(git symbolic-ref --short HEAD)
 
-# Iterate through each local branch and check if it exists in the list of merged branches
-for branch in $(git for-each-ref --format='%(refname:short)' refs/heads); do
-  if ! echo "$merged_branches" | grep -q "^$branch$"; then
-    if [ "$force_delete" = true ]; then
-      echo "Force deleting branch '$branch' as it either doesn't exist on the origin or isn't merged."
-      git branch -D "$branch" 2>/dev/null || echo "Error: Could not delete branch '$branch'."
-    else
-      echo "Skipping branch '$branch' as it either doesn't exist on the origin or isn't merged."
-    fi
-  else
-    echo "Deleting branch '$branch' as it is merged and doesn't exist on the origin."
-    git branch -d "$branch" 2>/dev/null || echo "Error: Could not delete branch '$branch'."
+# Delete local branches that have been merged into the current branch
+git branch --merged | while read -r branch; do
+  branch=$(echo "$branch" | tr -d '* ')
+  # Skip protected branches
+  if [[ "$branch" == "main" || "$branch" == "master" || "$branch" == "$current_branch" ]]; then
+    continue
   fi
+  echo "Deleting merged branch '$branch'"
+  git branch -d "$branch" 2>/dev/null || echo "  Could not delete '$branch'"
 done
 
+# Optionally force-delete branches whose remote tracking branch is gone
+if [ "$force_delete" = true ]; then
+  git branch -vv | grep ': gone]' | while read -r line; do
+    branch=$(echo "$line" | awk '{print $1}')
+    if [[ "$branch" == "main" || "$branch" == "master" || "$branch" == "$current_branch" ]]; then
+      continue
+    fi
+    echo "Force deleting gone branch '$branch'"
+    git branch -D "$branch" 2>/dev/null || echo "  Could not delete '$branch'"
+  done
+fi

git/gitconfig

@@ -47,9 +47,9 @@
   lst  = diff HEAD^..HEAD         # Show changes in the last commit
 
   # Branch operations
-  sw   = checkout                 # Switch branches
-  swb  = checkout -b              # Create and switch to a branch
-  pd   = checkout -                # Jump to previous branch
+  sw   = switch                   # Switch branches
+  swb  = switch -c                # Create and switch to a branch
+  pd   = switch -                  # Jump to previous branch
   b    = branch                   # List branches
   bd   = branch -d                # Delete branch
 
@@ -90,6 +90,7 @@
   excludesfile = ~/.gitignore
   autocrlf = input
   whitespace = trailing-space,space-before-tab
+	pager = delta
 [branch]
 	autosetupmerge = true
 	sort = -committerdate
@@ -122,11 +123,6 @@
 [push]
 	default = current
 	autoSetupRemote = true
-[ghi]
-	token = !security find-internet-password -a michaelbarton -s github.com -l 'ghi token' -w
-
-[core]
-	pager = delta
 
 [interactive]
 	diffFilter = delta --color-only

gitignore

@@ -89,7 +89,6 @@ htmlcov/
 
 # Rust
 target/
-Cargo.lock
 
 # Go
 *.test
@@ -103,7 +102,6 @@ Cargo.lock
 node_modules/
 .npm/
 .yarn/
-package-lock.json # Optional: remove if you want to track this
 
 # Python
 .venv/

markdown/md2docx.sh

@@ -9,4 +9,4 @@ IN_FILE=$1
 FILENAME=$(basename -- "$IN_FILE")
 FILENAME_NOEXT="${FILENAME%.*}"
 
-pandoc -o ${FILENAME_NOEXT}.docx -f markdown -t docx $IN_FILE
+pandoc -o "${FILENAME_NOEXT}.docx" -f markdown -t docx "$IN_FILE"

markdown/md2pdf.sh

@@ -9,4 +9,4 @@ IN_FILE=$1
 FILENAME=$(basename -- "$IN_FILE")
 FILENAME_NOEXT="${FILENAME%.*}"
 
-pandoc -o ${FILENAME_NOEXT}.pdf -f markdown -t pdf $IN_FILE
+pandoc -o "${FILENAME_NOEXT}.pdf" -f markdown -t pdf "$IN_FILE"