Use 'command' prefix to bypass user aliases in core functions

Addresses review feedback from @akinomyoga on PR Bash-it#2342.

**Problem:**
Users may have aliases like:
- `alias mv='mv -i'` (prompts for confirmation)
- `alias grep='grep --color=always'` (breaks parsing)
- `alias rm='rm -i'` (prompts for confirmation)

These aliases can break bash-it core functions that assume standard
command behavior.

**Solution:**
Prefix sensitive commands with `command` to bypass aliases:
- `command mv` - ensures atomic file operations without prompts
- `command grep` - ensures predictable output format
- Applied to all mv/grep calls in doctor functions

**Documentation:**
Added coding standard to CLAUDE.md:
- Documents the `command` prefix pattern
- Lists common commands that should be prefixed
- Explains why this prevents surprises in core functions

This is a defensive programming practice that makes bash-it more
robust against varied user configurations.

Thanks to @akinomyoga for catching this!

Related to PR Bash-it#2342

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>

Author: seefood

CLAUDE.md

@@ -134,3 +134,9 @@ bash-it search docker
 - Follow existing code style in the repository
 - Add appropriate metadata using composure functions
 - Components should handle missing dependencies gracefully
+- **Prefix sensitive commands with `command`** to bypass user aliases:
+  - `command mv` instead of `mv` (users may have `alias mv='mv -i'`)
+  - `command grep` instead of `grep` (users may have custom grep flags)
+  - `command rm` instead of `rm` (users may have `alias rm='rm -i'`)
+  - Apply to any command that could be aliased and break core functionality
+  - This prevents surprises from user's alias configurations in bash-it core functions

lib/helpers.bash

@@ -423,7 +423,7 @@ function _bash-it-doctor-check-profile-sourcing-grep() {
 	[[ ! -f "$profile_file" ]] && return 1
 
 	# Look for common patterns that source .bashrc
-	grep -qE '(source|\.)\s+(~|\$HOME|"\$HOME")?/\.bashrc|if.*BASH_VERSION.*bashrc' "$profile_file"
+	command grep -qE '(source|\.)\s+(~|\$HOME|"\$HOME")?/\.bashrc|if.*BASH_VERSION.*bashrc' "$profile_file"
 }
 
 function _bash-it-doctor-check-profile-sourcing-test() {
@@ -446,10 +446,10 @@ function _bash-it-doctor-check-profile-sourcing-test() {
 	output=$(bash -l -c ':' 2>&1)
 
 	# Restore immediately
-	mv "$backup_bashrc" "$bashrc"
+	command mv "$backup_bashrc" "$bashrc"
 
 	# Check if our marker appeared
-	grep -q "__BASHRC_WAS_SOURCED__" <<< "$output"
+	command grep -q "__BASHRC_WAS_SOURCED__" <<< "$output"
 }
 
 function _bash-it-doctor-check-profile-sourcing() {
@@ -578,7 +578,7 @@ function _bash-it-doctor-summary() {
 		# Offer to update if behind and it's safe to do so
 		local git_status untracked_files merge_base can_ff
 		git_status="$(git status --porcelain 2> /dev/null)"
-		untracked_files="$(echo "$git_status" | grep -c '^??' || true)"
+		untracked_files="$(echo "$git_status" | command grep -c '^??' || true)"
 
 		# Check if we can fast-forward
 		merge_base="$(git merge-base HEAD "${BASH_IT_REMOTE}/${BASH_IT_DEVELOPMENT_BRANCH}" 2> /dev/null)"
@@ -590,7 +590,7 @@ function _bash-it-doctor-summary() {
 		# Only offer merge if:
 		# 1. No modified/staged files (untracked are OK)
 		# 2. Can fast-forward OR no untracked files that would conflict
-		if ! echo "$git_status" | grep -v '^??' -q; then
+		if ! echo "$git_status" | command grep -v '^??' -q; then
 			if [[ "$can_ff" == "true" ]] || [[ "$untracked_files" == "0" ]]; then
 				echo ""
 				echo "Would you like to update now? This will merge ${BASH_IT_REMOTE}/${BASH_IT_DEVELOPMENT_BRANCH} into your current branch."
@@ -635,9 +635,9 @@ function _bash-it-doctor-summary() {
 
 	if [[ ${#config_files_to_check[@]} -gt 0 ]]; then
 		for config_file_path in "${config_files_to_check[@]}"; do
-			if grep -i "bash.it\|bash_it" "$config_file_path" > /dev/null 2>&1; then
+			if command grep -i "bash.it\|bash_it" "$config_file_path" > /dev/null 2>&1; then
 				echo "From ${config_file_path}:"
-				grep -n -i "bash.it\|bash_it" -B2 -A2 "$config_file_path" 2> /dev/null
+				command grep -n -i "bash.it\|bash_it" -B2 -A2 "$config_file_path" 2> /dev/null
 				echo ""
 			fi
 		done