fix: address PR 162 regressions

Author: helizaga

lib/adapters.sh

@@ -166,10 +166,7 @@ editor_open() {
     target="$workspace"
   fi
 
-  # Split multi-word commands (e.g., "code --wait") into an array for safe execution
-  local _cmd_arr
-  read -ra _cmd_arr <<< "$GTR_EDITOR_CMD"
-  "${_cmd_arr[@]}" "$target"
+  _run_configured_command "$GTR_EDITOR_CMD" "$target"
 }
 
 # Globals set by load_ai_adapter: GTR_AI_CMD, GTR_AI_CMD_NAME
@@ -180,10 +177,20 @@ ai_can_start() {
 ai_start() {
   local path="$1"
   shift
-  # Split multi-word commands (e.g., "bunx @github/copilot@latest") into an array for safe execution
-  local _cmd_arr
-  read -ra _cmd_arr <<< "$GTR_AI_CMD"
-  (cd "$path" && "${_cmd_arr[@]}" "$@")
+  (cd "$path" && _run_configured_command "$GTR_AI_CMD" "$@")
+}
+
+# Parse and run a config-supplied command string while preserving quoted args.
+_run_configured_command() {
+  local command_string="$1"
+  shift
+  local extra_args=("$@")
+
+  (
+    eval "set -- $command_string" || exit 1
+    [ "$#" -gt 0 ] || exit 1
+    "$@" "${extra_args[@]}"
+  )
 }
 
 # Standard AI adapter builder — used by adapter files that follow the common pattern
@@ -297,23 +304,21 @@ resolve_workspace_file() {
 # Usage: _load_adapter <type> <name> <label> <builtin_list> <path_hint>
 _load_adapter() {
   local type="$1" name="$2" label="$3" builtin_list="$4" path_hint="$5"
+  local adapter_selector="${name%% *}"
 
-  # Reject adapter names containing path traversal characters
-  case "$name" in
-    */* | *..* | *\\*)
-      log_error "$label name '$name' contains invalid characters"
-      return 1
-      ;;
-  esac
-
-  local adapter_file="$GTR_DIR/adapters/${type}/${name}.sh"
+  local adapter_file="$GTR_DIR/adapters/${type}/${adapter_selector}.sh"
 
   # 1. Try loading explicit adapter file (custom overrides like claude, nano)
-  if [ -f "$adapter_file" ]; then
-    # shellcheck disable=SC1090
-    . "$adapter_file"
-    return 0
-  fi
+  case "$adapter_selector" in
+    */* | *..* | *\\*) ;;
+    *)
+      if [ -f "$adapter_file" ]; then
+        # shellcheck disable=SC1090
+        . "$adapter_file"
+        return 0
+      fi
+      ;;
+  esac
 
   # 2. Try registry lookup (declarative adapters)
   local registry entry

lib/commands/init.sh

@@ -65,10 +65,11 @@ cmd_init() {
       ;;
   esac
 
-  # Generate output (cached to ~/.cache/gtr/, auto-invalidates on version change)
+  # Generate output (cached to ~/.cache/gtr/, auto-invalidates on shell integration changes)
   local cache_dir="${XDG_CACHE_HOME:-$HOME/.cache}/gtr"
   local cache_file="$cache_dir/init-${func_name}.${shell}"
-  local cache_stamp="# gtr-cache: version=${GTR_VERSION:-unknown} func=$func_name shell=$shell"
+  local cache_schema="${GTR_INIT_CACHE_VERSION:-2}"
+  local cache_stamp="# gtr-cache: version=${GTR_VERSION:-unknown} init=${cache_schema} func=$func_name shell=$shell"
 
   # Return cached output if version matches
   if [ -f "$cache_file" ]; then
@@ -94,6 +95,26 @@ _init_bash() {
 # git-gtr shell integration (cached to ~/.cache/gtr/)
 # Setup: see git gtr help init
 
+__FUNC___gtrconfig_path() {
+  local _gtr_git_common_dir _gtr_repo_root
+  _gtr_git_common_dir="$(git rev-parse --git-common-dir 2>/dev/null)" || return 1
+
+  if [ "$_gtr_git_common_dir" = ".git" ]; then
+    _gtr_repo_root="$(git rev-parse --show-toplevel 2>/dev/null)" || return 1
+  else
+    _gtr_repo_root="${_gtr_git_common_dir%/.git}"
+  fi
+
+  printf '%s/.gtrconfig\n' "$_gtr_repo_root"
+}
+
+__FUNC___hooks_hash() {
+  local _gtr_config_file="$1"
+  local _gtr_hook_defs
+  _gtr_hook_defs="$(git config -f "$_gtr_config_file" --get-regexp '^hooks\.' 2>/dev/null)" || return 1
+  printf '%s\n' "$_gtr_hook_defs" | shasum -a 256 | cut -d' ' -f1
+}
+
 __FUNC___run_post_cd_hooks() {
   local dir="$1"
   local _gtr_trust_dir="${XDG_CONFIG_HOME:-$HOME/.config}/gtr/trusted"
@@ -105,14 +126,14 @@ __FUNC___run_post_cd_hooks() {
     # Read from git config (local > global > system)
     _gtr_hooks="$(git config --get-all gtr.hook.postCd 2>/dev/null)" || true
     # Read from .gtrconfig if it exists — only if trusted
-    _gtr_config_file="$(git rev-parse --show-toplevel 2>/dev/null)/.gtrconfig"
+    _gtr_config_file="$(__FUNC___gtrconfig_path 2>/dev/null)" || true
     if [ -f "$_gtr_config_file" ]; then
       local _gtr_file_hooks
       _gtr_file_hooks="$(git config -f "$_gtr_config_file" --get-all hooks.postCd 2>/dev/null)" || true
       if [ -n "$_gtr_file_hooks" ]; then
         # Verify trust before including .gtrconfig hooks
         local _gtr_hook_hash
-        _gtr_hook_hash="$(git config -f "$_gtr_config_file" --get-regexp '^hooks\.' 2>/dev/null | shasum -a 256 | cut -d' ' -f1)" || true
+        _gtr_hook_hash="$(__FUNC___hooks_hash "$_gtr_config_file" 2>/dev/null)" || true
         if [ -n "$_gtr_hook_hash" ] && [ -f "$_gtr_trust_dir/$_gtr_hook_hash" ]; then
           if [ -n "$_gtr_hooks" ]; then
             _gtr_hooks="$_gtr_hooks"$'\n'"$_gtr_file_hooks"
@@ -253,7 +274,7 @@ ___FUNC___completion() {
 
   if [ "$COMP_CWORD" -eq 1 ]; then
     # First argument: cd + all git-gtr subcommands
-    COMPREPLY=($(compgen -W "cd new go run copy editor ai rm mv rename ls list clean doctor adapter config completion init help version" -- "$cur"))
+    COMPREPLY=($(compgen -W "cd new go run copy editor ai rm mv rename ls list clean doctor adapter config completion init trust help version" -- "$cur"))
   elif [ "${COMP_WORDS[1]}" = "cd" ] && [ "$COMP_CWORD" -eq 2 ]; then
     # Worktree names for cd
     local worktrees
@@ -278,6 +299,28 @@ _init_zsh() {
 # git-gtr shell integration (cached to ~/.cache/gtr/)
 # Setup: see git gtr help init
 
+__FUNC___gtrconfig_path() {
+  emulate -L zsh
+  local _gtr_git_common_dir _gtr_repo_root
+  _gtr_git_common_dir="$(git rev-parse --git-common-dir 2>/dev/null)" || return 1
+
+  if [ "$_gtr_git_common_dir" = ".git" ]; then
+    _gtr_repo_root="$(git rev-parse --show-toplevel 2>/dev/null)" || return 1
+  else
+    _gtr_repo_root="${_gtr_git_common_dir%/.git}"
+  fi
+
+  printf '%s/.gtrconfig\n' "$_gtr_repo_root"
+}
+
+__FUNC___hooks_hash() {
+  emulate -L zsh
+  local _gtr_config_file="$1"
+  local _gtr_hook_defs
+  _gtr_hook_defs="$(git config -f "$_gtr_config_file" --get-regexp '^hooks\.' 2>/dev/null)" || return 1
+  printf '%s\n' "$_gtr_hook_defs" | shasum -a 256 | cut -d' ' -f1
+}
+
 __FUNC___run_post_cd_hooks() {
   emulate -L zsh
   local dir="$1"
@@ -290,14 +333,14 @@ __FUNC___run_post_cd_hooks() {
     # Read from git config (local > global > system)
     _gtr_hooks="$(git config --get-all gtr.hook.postCd 2>/dev/null)" || true
     # Read from .gtrconfig if it exists — only if trusted
-    _gtr_config_file="$(git rev-parse --show-toplevel 2>/dev/null)/.gtrconfig"
+    _gtr_config_file="$(__FUNC___gtrconfig_path 2>/dev/null)" || true
     if [ -f "$_gtr_config_file" ]; then
       local _gtr_file_hooks
       _gtr_file_hooks="$(git config -f "$_gtr_config_file" --get-all hooks.postCd 2>/dev/null)" || true
       if [ -n "$_gtr_file_hooks" ]; then
         # Verify trust before including .gtrconfig hooks
         local _gtr_hook_hash
-        _gtr_hook_hash="$(git config -f "$_gtr_config_file" --get-regexp '^hooks\.' 2>/dev/null | shasum -a 256 | cut -d' ' -f1)" || true
+        _gtr_hook_hash="$(__FUNC___hooks_hash "$_gtr_config_file" 2>/dev/null)" || true
         if [ -n "$_gtr_hook_hash" ] && [ -f "$_gtr_trust_dir/$_gtr_hook_hash" ]; then
           if [ -n "$_gtr_hooks" ]; then
             _gtr_hooks="$_gtr_hooks"$'\n'"$_gtr_file_hooks"
@@ -465,6 +508,26 @@ _init_fish() {
 # Add to ~/.config/fish/config.fish:
 #   git gtr init fish | source
 
+function __FUNC___gtrconfig_path
+  set -l _gtr_git_common_dir (git rev-parse --git-common-dir 2>/dev/null)
+  test -n "$_gtr_git_common_dir"; or return 1
+
+  if test "$_gtr_git_common_dir" = ".git"
+    set -l _gtr_repo_root (git rev-parse --show-toplevel 2>/dev/null)
+    test -n "$_gtr_repo_root"; or return 1
+    printf '%s/.gtrconfig\n' "$_gtr_repo_root"
+  else
+    printf '%s/.gtrconfig\n' (string replace -r '/\\.git$' '' -- "$_gtr_git_common_dir")
+  end
+end
+
+function __FUNC___hooks_hash
+  set -l _gtr_config_file "$argv[1]"
+  set -l _gtr_hook_defs (git config -f "$_gtr_config_file" --get-regexp '^hooks\.' 2>/dev/null)
+  test $status -eq 0; or return 1
+  printf '%s\n' "$_gtr_hook_defs" | shasum -a 256 | cut -d' ' -f1
+end
+
 function __FUNC___run_post_cd_hooks
   set -l dir "$argv[1]"
   set -l _gtr_trust_dir "$HOME/.config/gtr/trusted"
@@ -478,13 +541,13 @@ function __FUNC___run_post_cd_hooks
     # Read from git config (local > global > system)
     set -l _gtr_git_hooks (git config --get-all gtr.hook.postCd 2>/dev/null)
     # Read from .gtrconfig if it exists — only if trusted
-    set -l _gtr_config_file (git rev-parse --show-toplevel 2>/dev/null)"/.gtrconfig"
+    set -l _gtr_config_file (__FUNC___gtrconfig_path 2>/dev/null)
     set -l _gtr_file_hooks
     if test -f "$_gtr_config_file"
       set -l _gtr_candidate_hooks (git config -f "$_gtr_config_file" --get-all hooks.postCd 2>/dev/null)
       if test (count $_gtr_candidate_hooks) -gt 0
         # Verify trust before including .gtrconfig hooks
-        set -l _gtr_hook_hash (git config -f "$_gtr_config_file" --get-regexp '^hooks\.' 2>/dev/null | shasum -a 256 | cut -d' ' -f1)
+        set -l _gtr_hook_hash (__FUNC___hooks_hash "$_gtr_config_file" 2>/dev/null)
         if test -n "$_gtr_hook_hash"; and test -f "$_gtr_trust_dir/$_gtr_hook_hash"
           set _gtr_file_hooks $_gtr_candidate_hooks
         else

lib/commands/trust.sh

@@ -33,8 +33,12 @@ cmd_trust() {
   log_warn "These commands will execute on your machine during gtr operations."
 
   if prompt_yes_no "Trust these hooks?"; then
-    _hooks_mark_trusted "$config_file"
-    log_info "Hooks marked as trusted"
+    if _hooks_mark_trusted "$config_file"; then
+      log_info "Hooks marked as trusted"
+    else
+      log_error "Failed to mark hooks as trusted"
+      return 1
+    fi
   else
     log_info "Hooks remain untrusted and will not execute"
   fi

lib/copy.sh

@@ -282,14 +282,21 @@ _apply_directory_excludes() {
         local pattern_prefix="${exclude_pattern%%/*}"
         local pattern_suffix="${exclude_pattern#*/}"
 
-        # Reject bare glob-only suffixes that would match everything
+        # Reject empty suffixes and protect Git metadata from removal
         case "$pattern_suffix" in
-          ""|"*"|"**"|".*")
+          "")
             log_warn "Skipping overly broad exclude suffix: $exclude_pattern"
             continue
             ;;
         esac
 
+        case "$exclude_pattern" in
+          .git|*/.git|.git/*|*/.git/*)
+            log_warn "Skipping exclude pattern targeting .git metadata: $exclude_pattern"
+            continue
+            ;;
+        esac
+
         # Intentional glob pattern matching for directory prefix
         # shellcheck disable=SC2254
         case "$dir_path" in

lib/hooks.sh

@@ -20,7 +20,16 @@ _hooks_file_hash() {
   if [ -z "$hook_content" ]; then
     return 1
   fi
-  printf '%s' "$hook_content" | shasum -a 256 | cut -d' ' -f1
+  printf '%s\n' "$hook_content" | shasum -a 256 | cut -d' ' -f1
+}
+
+# Resolve the trust marker path for a .gtrconfig file
+# Usage: _hooks_trust_path <config_file>
+_hooks_trust_path() {
+  local config_file="$1"
+  local hash
+  hash=$(_hooks_file_hash "$config_file") || return 1
+  printf '%s/%s\n' "$_GTR_TRUST_DIR" "$hash"
 }
 
 # Check if .gtrconfig hooks are trusted for the current repository
@@ -30,21 +39,21 @@ _hooks_are_trusted() {
   local config_file="$1"
   [ ! -f "$config_file" ] && return 0
 
-  local hash
-  hash=$(_hooks_file_hash "$config_file") || return 0  # no hooks = trusted
+  local trust_path
+  trust_path=$(_hooks_trust_path "$config_file") || return 0  # no hooks = trusted
 
-  [ -f "$_GTR_TRUST_DIR/$hash" ]
+  [ -f "$trust_path" ]
 }
 
 # Mark .gtrconfig hooks as trusted
 # Usage: _hooks_mark_trusted <config_file>
 _hooks_mark_trusted() {
   local config_file="$1"
-  local hash
-  hash=$(_hooks_file_hash "$config_file") || return 0
+  local trust_path
+  trust_path=$(_hooks_trust_path "$config_file") || return 0
 
   mkdir -p "$_GTR_TRUST_DIR"
-  printf '%s\n' "$config_file" > "$_GTR_TRUST_DIR/$hash"
+  printf '%s\n' "$config_file" > "$trust_path"
 }
 
 # Get hooks, filtering out untrusted .gtrconfig hooks with a warning

lib/platform.sh

@@ -126,32 +126,52 @@ spawn_terminal_in() {
       fi
       ;;
     linux)
-      # Escape cmd and path for safe embedding in sh -c strings
-      local safe_sh_cmd safe_sh_path
-      safe_sh_cmd=$(printf '%q' "$cmd")
-      safe_sh_path=$(printf '%q' "$path")
+      local shell_after="${SHELL:-/bin/sh}"
+      # shellcheck disable=SC2016 # The script is intentionally evaluated by sh in the new terminal.
+      local terminal_script='cd "$1" || exit 1
+shift
+if [ "$#" -gt 0 ]; then
+  "$@"
+fi
+exec "$SHELL_AFTER"'
       # Try common terminal emulators
       if command -v gnome-terminal >/dev/null 2>&1; then
-        gnome-terminal --working-directory="$path" --title="$title" -- sh -c "$safe_sh_cmd; exec \$SHELL" 2>/dev/null || true
+        if [ -n "$cmd" ]; then
+          gnome-terminal --working-directory="$path" --title="$title" -- env SHELL_AFTER="$shell_after" sh -c "$terminal_script" sh "$path" bash -lc "$cmd" 2>/dev/null || true
+        else
+          gnome-terminal --working-directory="$path" --title="$title" -- env SHELL_AFTER="$shell_after" sh -c "$terminal_script" sh "$path" 2>/dev/null || true
+        fi
       elif command -v konsole >/dev/null 2>&1; then
-        konsole --workdir "$path" -p "tabtitle=$title" -e sh -c "$safe_sh_cmd; exec \$SHELL" 2>/dev/null || true
+        if [ -n "$cmd" ]; then
+          konsole --workdir "$path" -p "tabtitle=$title" -e env SHELL_AFTER="$shell_after" sh -c "$terminal_script" sh "$path" bash -lc "$cmd" 2>/dev/null || true
+        else
+          konsole --workdir "$path" -p "tabtitle=$title" -e env SHELL_AFTER="$shell_after" sh -c "$terminal_script" sh "$path" 2>/dev/null || true
+        fi
       elif command -v xterm >/dev/null 2>&1; then
-        xterm -T "$title" -e "cd $safe_sh_path && $safe_sh_cmd && exec \$SHELL" 2>/dev/null || true
+        if [ -n "$cmd" ]; then
+          xterm -T "$title" -e env SHELL_AFTER="$shell_after" sh -c "$terminal_script" sh "$path" bash -lc "$cmd" 2>/dev/null || true
+        else
+          xterm -T "$title" -e env SHELL_AFTER="$shell_after" sh -c "$terminal_script" sh "$path" 2>/dev/null || true
+        fi
       else
         log_warn "No supported terminal emulator found"
         return 1
       fi
       ;;
     windows)
-      # Escape for safe embedding in cmd.exe strings
-      local safe_win_cmd safe_win_path
-      safe_win_cmd=$(printf '%q' "$cmd")
-      safe_win_path=$(printf '%q' "$path")
       # Try Windows Terminal, then fallback to cmd
       if command -v wt >/dev/null 2>&1; then
-        wt -d "$path" "$cmd" 2>/dev/null || true
+        if [ -n "$cmd" ]; then
+          wt -d "$path" cmd.exe /k "$cmd" 2>/dev/null || true
+        else
+          wt -d "$path" 2>/dev/null || true
+        fi
       else
-        cmd.exe /c start "$title" cmd.exe /k "cd /d $safe_win_path && $safe_win_cmd" 2>/dev/null || true
+        if [ -n "$cmd" ]; then
+          cmd.exe /c start "$title" cmd.exe /k "cd /d \"$path\" && $cmd" 2>/dev/null || true
+        else
+          cmd.exe /c start "$title" cmd.exe /k "cd /d \"$path\"" 2>/dev/null || true
+        fi
       fi
       ;;
     *)