config command now supports common/scripts

3 files changed, 133 insertions, 161 deletions

diff --git a/README.md b/README.md
index a0e61cc..ab38f79 100644
--- a/README.md
+++ b/README.md
@@ -114,7 +114,7 @@ Copy and paste the following snippet to any profile/startup file ie. `~/.bashrc`
 ```bash
 # Dotfiles Management System
 if [[ -d "$HOME/.cfg" && -d "$HOME/.cfg/refs" ]]; then
-    # Core git wrapper with repository as work-tree
+    # Core git wrapper - .cfg is bare repo, work-tree points to .cfg itself
     _config() {
         git --git-dir="$HOME/.cfg" --work-tree="$HOME/.cfg" "$@"
     }
@@ -163,7 +163,9 @@ if [[ -d "$HOME/.cfg" && -d "$HOME/.cfg/refs" ]]; then
         fi
 
         case "$repo_path" in
-            # Common configs → OS-specific config dirs
+            common/scripts/*)
+                echo "$HOME/.scripts/${repo_path#common/scripts/}"
+                ;;
             common/config/*)
                 case "$CFG_OS" in
                     linux)
@@ -174,6 +176,7 @@ if [[ -d "$HOME/.cfg" && -d "$HOME/.cfg/refs" ]]; then
                         echo "$HOME/Library/Application Support/${repo_path#common/config/}"
                         ;;
                     windows)
+                        # Windows Bash (Git Bash, MSYS, WSL) respects LOCALAPPDATA
                         echo "$LOCALAPPDATA\\${repo_path#common/config/}"
                         ;;
                     *)
@@ -181,32 +184,18 @@ if [[ -d "$HOME/.cfg" && -d "$HOME/.cfg/refs" ]]; then
                         ;;
                 esac
                 ;;
-
-            # Common assets → stay in repo
-            common/assets/*)
+            common/assets/*|profile/*|README.md)
                 echo "$HOME/.cfg/$repo_path"
                 ;;
-
-            # Other common files (dotfiles like .bashrc, .gitconfig, etc.) → $HOME
             common/*)
-                echo "$HOME/${repo_path#common/}"
+                echo "$HOME/.cfg/$repo_path"
                 ;;
-
-            # OS-specific home
             */home/*)
                 echo "$HOME/${repo_path#*/home/}"
                 ;;
-
-            # Profile configs and README → stay in repo
-            profile/*|README.md)
+            *)
                 echo "$HOME/.cfg/$repo_path"
                 ;;
-
-            # Default fallback
-            *)
-              echo "$HOME/.cfg/$repo_path"
-              ;;
-
         esac
     }
 
@@ -232,6 +221,7 @@ if [[ -d "$HOME/.cfg" && -d "$HOME/.cfg/refs" ]]; then
     config() {
         local cmd="$1"; shift
         local target_dir=""
+
         # Parse optional --target flag for add
         if [[ "$cmd" == "add" ]]; then
             while [[ "$1" == --* ]]; do
@@ -251,7 +241,29 @@ if [[ -d "$HOME/.cfg" && -d "$HOME/.cfg/refs" ]]; then
         case "$cmd" in
             add)
                 local file_path
-                for file_path in "$@"; do
+                local git_opts=()
+                local files=()
+
+                # Parse arguments
+                while [[ $# -gt 0 ]]; do
+                    case "$1" in
+                        --target|-t)
+                            target_dir="$2"
+                            shift 2
+                            ;;
+                        -*)  # Any other flags are git flags
+                            git_opts+=("$1")
+                            shift
+                            ;;
+                        *)   # Anything else is a file
+                            files+=("$1")
+                            shift
+                            ;;
+                    esac
+                done
+
+                # Process each file
+                for file_path in "${files[@]}"; do
                     local repo_path
                     if [[ -n "$target_dir" ]]; then
                         local rel_path
@@ -269,11 +281,13 @@ if [[ -d "$HOME/.cfg" && -d "$HOME/.cfg/refs" ]]; then
                     mkdir -p "$(dirname "$full_repo_path")"
                     cp -a "$file_path" "$full_repo_path"
 
-                    git --git-dir="$HOME/.cfg" --work-tree="$HOME/.cfg" add "$repo_path"
+                    # Only git flags + repo_path go to git
+                    _config add "${git_opts[@]}" "$repo_path"
 
                     echo "Added: $file_path -> $repo_path"
                 done
                 ;;
+
             rm)
                 local rm_opts=""
                 local file_path_list=()
@@ -299,11 +313,13 @@ if [[ -d "$HOME/.cfg" && -d "$HOME/.cfg/refs" ]]; then
                     echo "Removed: $file_path"
                 done
                 ;;
+
             sync)
                 local direction="${1:-to-repo}"; shift
                 _config ls-files | while read -r repo_file; do
                     local sys_file="$(_sys_path "$repo_file")"
                     local full_repo_path="$HOME/.cfg/$repo_file"
+
                     if [[ "$direction" == "to-repo" ]]; then
                         if [[ -e "$sys_file" && -n "$(diff "$full_repo_path" "$sys_file" 2>/dev/null || echo "diff")" ]]; then
                             cp -a "$sys_file" "$full_repo_path"
@@ -324,18 +340,36 @@ if [[ -d "$HOME/.cfg" && -d "$HOME/.cfg/refs" ]]; then
                     fi
                 done
                 ;;
+
             status)
+                # Check for missing files and auto-sync existing ones
                 local auto_synced=()
+                local missing_files=()
+
                 while read -r repo_file; do
                     local sys_file="$(_sys_path "$repo_file")"
                     local full_repo_path="$HOME/.cfg/$repo_file"
-                    if [[ -e "$sys_file" && -e "$full_repo_path" ]]; then
+
+                    if [[ ! -e "$full_repo_path" ]]; then
+                        missing_files+=("$repo_file")
+                    elif [[ -e "$sys_file" ]]; then
                         if ! diff -q "$full_repo_path" "$sys_file" >/dev/null 2>&1; then
                             cp -fa "$sys_file" "$full_repo_path"
                             auto_synced+=("$repo_file")
                         fi
                     fi
                 done < <(_config ls-files)
+
+                # Report missing files
+                if [[ ${#missing_files[@]} -gt 0 ]]; then
+                    echo "=== Missing Files (consider removing from git) ==="
+                    for repo_file in "${missing_files[@]}"; do
+                        echo "missing: $repo_file"
+                    done
+                    echo
+                fi
+
+                # Report auto-synced files
                 if [[ ${#auto_synced[@]} -gt 0 ]]; then
                     echo "=== Auto-synced Files ==="
                     for repo_file in "${auto_synced[@]}"; do
@@ -343,13 +377,15 @@ if [[ -d "$HOME/.cfg" && -d "$HOME/.cfg/refs" ]]; then
                     done
                     echo
                 fi
+
                 _config status
-                echo
                 ;;
-            deploy)
+
+            deploy|checkout)
+                echo "Deploying dotfiles from .cfg..."
                 _config ls-files | while read -r repo_file; do
                     local full_repo_path="$HOME/.cfg/$repo_file"
-                    local sys_file="$(_sys_path "$repo_file")"  # destination only
+                    local sys_file="$(_sys_path "$repo_file")"
 
                     # Only continue if the source exists
                     if [[ -e "$full_repo_path" && -n "$sys_file" ]]; then
@@ -369,29 +405,7 @@ if [[ -d "$HOME/.cfg" && -d "$HOME/.cfg/refs" ]]; then
                     fi
                 done
                 ;;
-            checkout)
-                echo "Checking out dotfiles from .cfg..."
-                _config ls-files | while read -r repo_file; do
-                    local full_repo_path="$HOME/.cfg/$repo_file"
-                    local sys_file="$(_sys_path "$repo_file")"
-
-                    if [[ -e "$full_repo_path" && -n "$sys_file" ]]; then
-                        local dest_dir
-                        dest_dir="$(dirname "$sys_file")"
 
-                        # Create destination if it doesn't exist
-                        if [[ "$sys_file" == /* && "$sys_file" != "$HOME/"* ]]; then
-                            _sudo_prompt mkdir -p "$dest_dir"
-                            _sudo_prompt cp -a "$full_repo_path" "$sys_file"
-                        else
-                            mkdir -p "$dest_dir"
-                            cp -a "$full_repo_path" "$sys_file"
-                        fi
-
-                        echo "Checked out: $repo_file -> $sys_file"
-                    fi
-                done
-                ;;
             backup)
                 local timestamp=$(date +%Y%m%d%H%M%S)
                 local backup_dir="$HOME/.dotfiles_backup/$timestamp"
@@ -407,6 +421,7 @@ if [[ -d "$HOME/.cfg" && -d "$HOME/.cfg/refs" ]]; then
                 done
                 echo "Backup complete. To restore, copy files from $backup_dir to their original locations."
                 ;;
+
             *)
                 _config "$cmd" "$@"
                 ;;
diff --git a/common/config/zsh/user/functions.zsh b/common/config/zsh/user/functions.zsh
index b4fa1c3..7c79ee5 100644
--- a/common/config/zsh/user/functions.zsh
+++ b/common/config/zsh/user/functions.zsh
@@ -1,6 +1,5 @@
 # Dotfiles Management System
 if [[ -d "$HOME/.cfg" && -d "$HOME/.cfg/refs" ]]; then
-
     # Core git wrapper - .cfg is bare repo, work-tree points to .cfg itself
     _config() {
         git --git-dir="$HOME/.cfg" --work-tree="$HOME/.cfg" "$@"
@@ -18,13 +17,13 @@ if [[ -d "$HOME/.cfg" && -d "$HOME/.cfg/refs" ]]; then
     _repo_path() {
         local f="$1"
 
-        # Absolute paths outside HOME
+        # If it's an absolute path that's not in HOME, handle it specially
         if [[ "$f" == /* && "$f" != "$HOME/"* ]]; then
             echo "$CFG_OS/${f#/}"
             return
         fi
 
-        # Files already in repo structure
+        # Check for paths that should go to the repository root
         case "$f" in
             common/*|linux/*|macos/*|windows/*|profile/*|README.md)
                 echo "$f"
@@ -35,12 +34,19 @@ if [[ -d "$HOME/.cfg" && -d "$HOME/.cfg/refs" ]]; then
                 ;;
         esac
 
-        # Default: OS-specific home
+        # Default: put under OS-specific home
         echo "$CFG_OS/home/$f"
     }
 
     _sys_path() {
         local repo_path="$1"
+        local os_path_pattern="$CFG_OS/"
+
+        # Handle OS-specific files that are not in the home subdirectory
+        if [[ "$repo_path" == "$os_path_pattern"* && "$repo_path" != */home/* ]]; then
+            echo "/${repo_path#$os_path_pattern}"
+            return
+        fi
 
         case "$repo_path" in
             common/scripts/*)
@@ -261,70 +267,6 @@ if [[ -d "$HOME/.cfg" && -d "$HOME/.cfg/refs" ]]; then
                 _config status
                 ;;
 
-            clean-missing)
-                echo "Removing missing files from git index..."
-                local removed_count=0
-                while read -r repo_file; do
-                    local full_repo_path="$HOME/.cfg/$repo_file"
-                    if [[ ! -e "$full_repo_path" ]]; then
-                        _config rm --cached "$repo_file"
-                        echo "Removed from git: $repo_file"
-                        ((removed_count++))
-                    fi
-                done < <(_config ls-files)
-                echo "Removed $removed_count missing files from git index."
-                ;;
-
-            move-files)
-                # Move files from one path pattern to another in the repository
-                local from_pattern="$1"
-                local to_pattern="$2"
-
-                if [[ -z "$from_pattern" || -z "$to_pattern" ]]; then
-                    echo "Usage: config move-files <from_pattern> <to_pattern>"
-                    echo "Example: config move-files 'common/nvim' 'common/config/nvim'"
-                    return 1
-                fi
-
-                echo "Moving files from $from_pattern to $to_pattern..."
-                local moved_count=0
-
-                # Find all files matching the from_pattern
-                _config ls-files | grep "^$from_pattern/" | while read -r repo_file; do
-                    local new_repo_file="${repo_file/$from_pattern/$to_pattern}"
-                    local old_full_path="$HOME/.cfg/$repo_file"
-                    local new_full_path="$HOME/.cfg/$new_repo_file"
-
-                    # Create destination directory
-                    mkdir -p "$(dirname "$new_full_path")"
-
-                    # Move the file in the filesystem if it exists
-                    if [[ -e "$old_full_path" ]]; then
-                        mv "$old_full_path" "$new_full_path"
-                        echo "Moved: $repo_file -> $new_repo_file"
-                    else
-                        # File doesn't exist, but we still need to update git index
-                        # Try to get it from the system location first
-                        local sys_file="$(_sys_path "$repo_file")"
-                        if [[ -e "$sys_file" ]]; then
-                            cp -a "$sys_file" "$new_full_path"
-                            echo "Copied from system: $sys_file -> $new_repo_file"
-                        else
-                            echo "Warning: Neither repo nor system file exists for $repo_file"
-                            continue
-                        fi
-                    fi
-
-                    # Update git index
-                    _config rm --cached "$repo_file" 2>/dev/null || true
-                    _config add "$new_repo_file"
-
-                    ((moved_count++))
-                done
-
-                echo "Moved $moved_count files from $from_pattern to $to_pattern"
-                ;;
-
             deploy|checkout)
                 echo "Deploying dotfiles from .cfg..."
                 _config ls-files | while read -r repo_file; do
diff --git a/common/install.sh b/common/install.sh
index 4a2b209..0fd7993 100755
--- a/common/install.sh
+++ b/common/install.sh
@@ -1277,7 +1277,7 @@ install_config_command() {
 
 # Dotfiles Management System
 if [[ -d "$HOME/.cfg" && -d "$HOME/.cfg/refs" ]]; then
-    # Core git wrapper with repository as work-tree
+    # Core git wrapper - .cfg is bare repo, work-tree points to .cfg itself
     _config() {
         git --git-dir="$HOME/.cfg" --work-tree="$HOME/.cfg" "$@"
     }
@@ -1326,7 +1326,9 @@ if [[ -d "$HOME/.cfg" && -d "$HOME/.cfg/refs" ]]; then
         fi
 
         case "$repo_path" in
-            # Common configs → OS-specific config dirs
+            common/scripts/*)
+                echo "$HOME/.scripts/${repo_path#common/scripts/}"
+                ;;
             common/config/*)
                 case "$CFG_OS" in
                     linux)
@@ -1337,6 +1339,7 @@ if [[ -d "$HOME/.cfg" && -d "$HOME/.cfg/refs" ]]; then
                         echo "$HOME/Library/Application Support/${repo_path#common/config/}"
                         ;;
                     windows)
+                        # Windows Bash (Git Bash, MSYS, WSL) respects LOCALAPPDATA
                         echo "$LOCALAPPDATA\\${repo_path#common/config/}"
                         ;;
                     *)
@@ -1344,32 +1347,18 @@ if [[ -d "$HOME/.cfg" && -d "$HOME/.cfg/refs" ]]; then
                         ;;
                 esac
                 ;;
-
-            # Common assets → stay in repo
-            common/assets/*)
+            common/assets/*|profile/*|README.md)
                 echo "$HOME/.cfg/$repo_path"
                 ;;
-
-            # Other common files (dotfiles like .bashrc, .gitconfig, etc.) → $HOME
             common/*)
-                echo "$HOME/${repo_path#common/}"
+                echo "$HOME/.cfg/$repo_path"
                 ;;
-
-            # OS-specific home
             */home/*)
                 echo "$HOME/${repo_path#*/home/}"
                 ;;
-
-            # Profile configs and README → stay in repo
-            profile/*|README.md)
+            *)
                 echo "$HOME/.cfg/$repo_path"
                 ;;
-
-            # Default fallback
-            *)
-              echo "$HOME/.cfg/$repo_path"
-              ;;
-
         esac
     }
 
@@ -1415,7 +1404,29 @@ if [[ -d "$HOME/.cfg" && -d "$HOME/.cfg/refs" ]]; then
         case "$cmd" in
             add)
                 local file_path
-                for file_path in "$@"; do
+                local git_opts=()
+                local files=()
+
+                # Parse arguments
+                while [[ $# -gt 0 ]]; do
+                    case "$1" in
+                        --target|-t)
+                            target_dir="$2"
+                            shift 2
+                            ;;
+                        -*)  # Any other flags are git flags
+                            git_opts+=("$1")
+                            shift
+                            ;;
+                        *)   # Anything else is a file
+                            files+=("$1")
+                            shift
+                            ;;
+                    esac
+                done
+
+                # Process each file
+                for file_path in "${files[@]}"; do
                     local repo_path
                     if [[ -n "$target_dir" ]]; then
                         local rel_path
@@ -1433,11 +1444,13 @@ if [[ -d "$HOME/.cfg" && -d "$HOME/.cfg/refs" ]]; then
                     mkdir -p "$(dirname "$full_repo_path")"
                     cp -a "$file_path" "$full_repo_path"
 
-                    git --git-dir="$HOME/.cfg" --work-tree="$HOME/.cfg" add "$repo_path"
+                    # Only git flags + repo_path go to git
+                    _config add "${git_opts[@]}" "$repo_path"
 
                     echo "Added: $file_path -> $repo_path"
                 done
                 ;;
+
             rm)
                 local rm_opts=""
                 local file_path_list=()
@@ -1463,11 +1476,13 @@ if [[ -d "$HOME/.cfg" && -d "$HOME/.cfg/refs" ]]; then
                     echo "Removed: $file_path"
                 done
                 ;;
+
             sync)
                 local direction="${1:-to-repo}"; shift
                 _config ls-files | while read -r repo_file; do
                     local sys_file="$(_sys_path "$repo_file")"
                     local full_repo_path="$HOME/.cfg/$repo_file"
+
                     if [[ "$direction" == "to-repo" ]]; then
                         if [[ -e "$sys_file" && -n "$(diff "$full_repo_path" "$sys_file" 2>/dev/null || echo "diff")" ]]; then
                             cp -a "$sys_file" "$full_repo_path"
@@ -1488,18 +1503,36 @@ if [[ -d "$HOME/.cfg" && -d "$HOME/.cfg/refs" ]]; then
                     fi
                 done
                 ;;
+
             status)
+                # Check for missing files and auto-sync existing ones
                 local auto_synced=()
+                local missing_files=()
+
                 while read -r repo_file; do
                     local sys_file="$(_sys_path "$repo_file")"
                     local full_repo_path="$HOME/.cfg/$repo_file"
-                    if [[ -e "$sys_file" && -e "$full_repo_path" ]]; then
+
+                    if [[ ! -e "$full_repo_path" ]]; then
+                        missing_files+=("$repo_file")
+                    elif [[ -e "$sys_file" ]]; then
                         if ! diff -q "$full_repo_path" "$sys_file" >/dev/null 2>&1; then
                             cp -fa "$sys_file" "$full_repo_path"
                             auto_synced+=("$repo_file")
                         fi
                     fi
                 done < <(_config ls-files)
+
+                # Report missing files
+                if [[ ${#missing_files[@]} -gt 0 ]]; then
+                    echo "=== Missing Files (consider removing from git) ==="
+                    for repo_file in "${missing_files[@]}"; do
+                        echo "missing: $repo_file"
+                    done
+                    echo
+                fi
+
+                # Report auto-synced files
                 if [[ ${#auto_synced[@]} -gt 0 ]]; then
                     echo "=== Auto-synced Files ==="
                     for repo_file in "${auto_synced[@]}"; do
@@ -1507,14 +1540,17 @@ if [[ -d "$HOME/.cfg" && -d "$HOME/.cfg/refs" ]]; then
                     done
                     echo
                 fi
+
                 _config status
-                echo
                 ;;
-            deploy)
+
+            deploy|checkout)
+                echo "Deploying dotfiles from .cfg..."
                 _config ls-files | while read -r repo_file; do
                     local full_repo_path="$HOME/.cfg/$repo_file"
                     local sys_file="$(_sys_path "$repo_file")"
 
+                    # Only continue if the source exists
                     if [[ -e "$full_repo_path" && -n "$sys_file" ]]; then
                         local dest_dir
                         dest_dir="$(dirname "$sys_file")"
@@ -1532,29 +1568,7 @@ if [[ -d "$HOME/.cfg" && -d "$HOME/.cfg/refs" ]]; then
                     fi
                 done
                 ;;
-            checkout)
-                echo "Checking out dotfiles from .cfg..."
-                _config ls-files | while read -r repo_file; do
-                    local full_repo_path="$HOME/.cfg/$repo_file"
-                    local sys_file="$(_sys_path "$repo_file")"
-
-                    if [[ -e "$full_repo_path" && -n "$sys_file" ]]; then
-                        local dest_dir
-                        dest_dir="$(dirname "$sys_file")"
 
-                        # Create destination if it doesn't exist
-                        if [[ "$sys_file" == /* && "$sys_file" != "$HOME/"* ]]; then
-                            _sudo_prompt mkdir -p "$dest_dir"
-                            _sudo_prompt cp -a "$full_repo_path" "$sys_file"
-                        else
-                            mkdir -p "$dest_dir"
-                            cp -a "$full_repo_path" "$sys_file"
-                        fi
-
-                        echo "Checked out: $repo_file -> $sys_file"
-                    fi
-                done
-                ;;
             backup)
                 local timestamp=$(date +%Y%m%d%H%M%S)
                 local backup_dir="$HOME/.dotfiles_backup/$timestamp"
@@ -1570,6 +1584,7 @@ if [[ -d "$HOME/.cfg" && -d "$HOME/.cfg/refs" ]]; then
                 done
                 echo "Backup complete. To restore, copy files from $backup_dir to their original locations."
                 ;;
+
             *)
                 _config "$cmd" "$@"
                 ;;