diff --git a/ansible/tasks/link_files.yml b/ansible/tasks/link_files.yml
index 208c7a54..f02572c9 100644
--- a/ansible/tasks/link_files.yml
+++ b/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" }
diff --git a/ansible/tasks/neovim.yml b/ansible/tasks/neovim.yml
index d663f399..76f91ae3 100644
--- a/ansible/tasks/neovim.yml
+++ b/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)
diff --git a/bash/bashrc b/bash/bashrc
index 135f70d1..2da82bac 100644
--- a/bash/bashrc
+++ b/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
diff --git a/fish/config.fish b/fish/config.fish
index 83e0ed7e..e30e007a 100644
--- a/fish/config.fish
+++ b/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
diff --git a/git/clean_branches.sh b/git/clean_branches.sh
index 7232c4ec..0fa1d717 100755
--- a/git/clean_branches.sh
+++ b/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
diff --git a/git/gitconfig b/git/gitconfig
index f562442a..508f0e02 100644
--- a/git/gitconfig
+++ b/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
diff --git a/gitignore b/gitignore
index 468b5bd0..83275666 100644
--- a/gitignore
+++ b/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/
diff --git a/lein/profiles.clj b/lein/profiles.clj
deleted file mode 100644
index db8e8237..00000000
--- a/lein/profiles.clj
+++ /dev/null
@@ -1,15 +0,0 @@
-{:user
- {:plugins       [[cider/cider-nrepl                  "0.8.2"]
-                  [com.jakemccrary/lein-test-refresh  "0.11.0"]
-                  [jonase/eastwood                    "0.2.3"]
-                  [lein-ancient                       "0.6.8"]]
-
-  :dependencies  [[clj-stacktrace   "0.2.8"]
-                  [spyscope         "0.1.5"]]
-
-  :injections    [(let [orig (ns-resolve (doto 'clojure.stacktrace require)
-                                         'print-cause-trace)
-                        new (ns-resolve (doto 'clj-stacktrace.repl require)
-                                        'pst)]
-                    (alter-var-root orig (constantly (deref new))))
-                  (require 'spyscope.core)]}}
diff --git a/markdown/md2docx.sh b/markdown/md2docx.sh
index 51901084..bcb9b4a1 100755
--- a/markdown/md2docx.sh
+++ b/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"
diff --git a/markdown/md2pdf.sh b/markdown/md2pdf.sh
index 89afb0e2..6956744a 100755
--- a/markdown/md2pdf.sh
+++ b/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"
diff --git a/mutt/muttrc b/mutt/muttrc
index 74c3c5d0..e3f8d978 100644
--- a/mutt/muttrc
+++ b/mutt/muttrc
@@ -5,7 +5,7 @@ set mbox_type = Maildir
 
 my_hdr X-URL: http://www.michaelbarton.me.uk
 
-set editor = "vim -f"
+set editor = "nvim"
 set mail_check = 60
 set timeout = 60
 set header_cache=~/.mutt/cache/headers
diff --git a/nvim/.neoconf.json b/nvim/.neoconf.json
index 7c480874..1d4389e6 100644
--- a/nvim/.neoconf.json
+++ b/nvim/.neoconf.json
@@ -1,10 +1,4 @@
 {
-  "neodev": {
-    "library": {
-      "enabled": true,
-      "plugins": true
-    }
-  },
   "neoconf": {
     "plugins": {
       "lua_ls": {
diff --git a/nvim/lua/config/lazy.lua b/nvim/lua/config/lazy.lua
index beeed76b..d4fcb0e2 100644
--- a/nvim/lua/config/lazy.lua
+++ b/nvim/lua/config/lazy.lua
@@ -38,6 +38,7 @@ require("lazy").setup({
 
     -- Import LazyVim extras - Editor utilities
     { import = "lazyvim.plugins.extras.editor.telescope" },
+    { import = "lazyvim.plugins.extras.editor.mini-move" },
     { import = "lazyvim.plugins.extras.util.project" },
 
     -- import/override with your plugins
diff --git a/nvim/lua/plugins/todo-comments.lua b/nvim/lua/plugins/todo-comments.lua
deleted file mode 100644
index f93cdb26..00000000
--- a/nvim/lua/plugins/todo-comments.lua
+++ /dev/null
@@ -1,22 +0,0 @@
--- Todo comments highlighting
-return {
-  "folke/todo-comments.nvim",
-  dependencies = { "nvim-lua/plenary.nvim" },
-  event = "VeryLazy",
-  opts = {
-    signs = true,
-    keywords = {
-      FIX = { icon = " ", color = "error", alt = { "FIXME", "BUG", "FIXIT", "ISSUE" } },
-      TODO = { icon = " ", color = "info" },
-      HACK = { icon = " ", color = "warning" },
-      WARN = { icon = " ", color = "warning", alt = { "WARNING", "XXX" } },
-      PERF = { icon = " ", alt = { "OPTIM", "PERFORMANCE", "OPTIMIZE" } },
-      NOTE = { icon = " ", color = "hint", alt = { "INFO" } },
-    },
-  },
-  keys = {
-    { "<leader>xt", "<cmd>TodoTrouble<cr>", desc = "Todo (Trouble)" },
-    { "<leader>xT", "<cmd>TodoTrouble keywords=TODO,FIX,FIXME<cr>", desc = "Todo/Fix/Fixme (Trouble)" },
-    { "<leader>st", "<cmd>TodoTelescope<cr>", desc = "Todo" },
-  },
-}
\ No newline at end of file
diff --git a/nvim/lua/plugins/trouble.lua b/nvim/lua/plugins/trouble.lua
index 7979b760..2ac7c182 100644
--- a/nvim/lua/plugins/trouble.lua
+++ b/nvim/lua/plugins/trouble.lua
@@ -1,14 +1,14 @@
--- Trouble - better diagnostics list
+-- Trouble - better diagnostics list (v3 API)
 return {
   "folke/trouble.nvim",
-  cmd = { "TroubleToggle", "Trouble" },
+  cmd = { "Trouble" },
   opts = {
     use_diagnostic_signs = true,
   },
   keys = {
-    { "<leader>xx", "<cmd>TroubleToggle document_diagnostics<cr>", desc = "Document Diagnostics (Trouble)" },
-    { "<leader>xX", "<cmd>TroubleToggle workspace_diagnostics<cr>", desc = "Workspace Diagnostics (Trouble)" },
-    { "<leader>xL", "<cmd>TroubleToggle loclist<cr>", desc = "Location List (Trouble)" },
-    { "<leader>xQ", "<cmd>TroubleToggle quickfix<cr>", desc = "Quickfix List (Trouble)" },
+    { "<leader>xx", "<cmd>Trouble diagnostics toggle filter.buf=0<cr>", desc = "Document Diagnostics (Trouble)" },
+    { "<leader>xX", "<cmd>Trouble diagnostics toggle<cr>", desc = "Workspace Diagnostics (Trouble)" },
+    { "<leader>xL", "<cmd>Trouble loclist toggle<cr>", desc = "Location List (Trouble)" },
+    { "<leader>xQ", "<cmd>Trouble qflist toggle<cr>", desc = "Quickfix List (Trouble)" },
   },
-}
\ No newline at end of file
+}
diff --git a/offlineimap/offlineimap.py b/offlineimap/offlineimap.py
index 6bc39ea5..4e8b4201 100644
--- a/offlineimap/offlineimap.py
+++ b/offlineimap/offlineimap.py
@@ -1,6 +1,4 @@
 import subprocess
-import re
-import sys
 
 
 def get_keychain_pass(account):
@@ -8,7 +6,9 @@ def get_keychain_pass(account):
     process = subprocess.Popen(command, stderr=subprocess.PIPE, stdout=subprocess.PIPE)
     process.wait()
     if process.returncode != 0:
-        raise RuntimeError("Error running command: \n".format(process.stderr.read().decode()))
+        raise RuntimeError(
+            "Error running command: {}".format(process.stderr.read().decode())
+        )
 
     password_block = process.stdout.read().decode().strip()
     if password_block:
@@ -19,5 +19,5 @@ def get_keychain_pass(account):
 
 
 def get_keyring_pass(key, value):
-    command = "secret-tool lookup {} {}".format(key, value)
-    return commands.getoutput(command).strip()
+    command = ["secret-tool", "lookup", key, value]
+    return subprocess.check_output(command).decode().strip()
diff --git a/parquet/csv_to_parquet.py b/parquet/csv_to_parquet.py
index 2d2302de..152607f9 100755
--- a/parquet/csv_to_parquet.py
+++ b/parquet/csv_to_parquet.py
@@ -12,11 +12,11 @@
 import pandas
 import sys
 
-IN_FILE, OUT_FILE = sys.argv[1], sys.argv[2]
-
-if not OUT_FILE:
-    print("Output file argument required.")
+if len(sys.argv) != 3:
+    print("Usage: csv_to_parquet <input.csv> <output.parquet>")
     exit(1)
 
+IN_FILE, OUT_FILE = sys.argv[1], sys.argv[2]
+
 data = pandas.read_csv(IN_FILE)
 data.to_parquet(OUT_FILE, index=False)
diff --git a/wgetrc b/wgetrc
index 22ba51ad..20840bce 100644
--- a/wgetrc
+++ b/wgetrc
@@ -1 +1 @@
-header = Contact: Michael Barton <mbarton@michaelbarton.me.uk>
+header = Contact: Michael Barton <mail@michaelbarton.me.uk>