--- a/portconf	2025-11-28 17:30:52.504350016 +0100
+++ b/portconf	2025-11-28 17:31:56.311870671 +0100
@@ -1,5 +1,5 @@
 #!/bin/bash
-# Copyright megabaks
+# Copyright megabaks (Modified by SpikyAtLinux)
 # Distributed under the terms of the GNU General Public License v3 or later
 ############################################################################
 ################ portage functions #########################################

--- a/portconf	2023-10-09 18:06:28.048896751 +0200
+++ b/portconf	2023-10-09 18:17:05.295858768 +0200
@@ -37,8 +37,8 @@
 sort_passed_uses(){
 	for opt in ${1};do
 		opt="${opt//\*/\\*}"
-		uses="$(tr "[:space:]" $'\n' <<< ${uses} | grep -v -e "^${opt#-}$" -e "^\-${opt#-}$" | tr $'\n' " ")"
-		uses+=" $(tr "[:space:]" $'\n' <<< ${1} | grep -e "^${opt#-}$" -e "^\-${opt#-}$" | tail -n1)"
+		uses="$(tr "[:space:]" $'\n' <<< ${uses} | grep -v -e "^${opt#-}$" -e "^-${opt#-}$" | tr $'\n' " ")"
+		uses+=" $(tr "[:space:]" $'\n' <<< ${1} | grep -e "^${opt#-}$" -e "^-${opt#-}$" | tail -n1)"
 		unset opt
 	done
 	echo ${uses}
@@ -811,7 +811,7 @@
 	set -f
 	FULL="${PROFILE} ${MAKE_USES}"
 	for opt in ${FULL};do
-		GLOBAL+=" $(echo ${FULL} | tr "[:space:]" $'\n' | grep -e "^${opt#-}$" -e "^\-${opt#-}$" | tail -n1)"
+		GLOBAL+=" $(echo ${FULL} | tr "[:space:]" $'\n' | grep -e "^${opt#-}$" -e "^-${opt#-}$" | tail -n1)"
 	done
 	GLOBAL="$(echo ${GLOBAL} | tr "[:space:]" $'\n' | sort -u)"
 ############################################################################
@@ -883,7 +883,7 @@
 
 				if grep -q "^${use}$" <<< "${GLOBAL}" && grep -q "^${use}$" <<< "${LOCAL}";then
 					global_use="${global_use} ${use}"
-				elif grep -q "^\-${use}$" <<< "${GLOBAL}" && grep -q "^\-${use}$" <<< "${LOCAL}";then
+				elif grep -q "^-${use}$" <<< "${GLOBAL}" && grep -q "^-${use}$" <<< "${LOCAL}";then
 					global_use="${global_use} -${use}"
 					incorrect_use="${incorrect_use// ${use}/}"
 				fi
@@ -1126,7 +1126,7 @@
 			if grep -q "^${flag}$" <<< "${USE}" && grep -q "^${flag}$" <<< "${PROFILE}";then
 				echo -e "Twice defined: ${red}${use}${restore}"
 				sed -e "s|[^[:punct:]]\<${flag}\>||g" -i ${tmp_file}
-			elif grep -q "^\-${flag}$" <<< "${USE}" && grep -q "^\-${flag}$" <<< "${PROFILE}";then
+			elif grep -q "^-${flag}$" <<< "${USE}" && grep -q "^-${flag}$" <<< "${PROFILE}";then
 				echo -e "Twice defined: ${red}-${use}${restore}"
 				sed -e "s|[^[:punct:]]\-\<${flag}\>||g" -i ${tmp_file}
 			fi
@@ -1811,11 +1811,11 @@
 --full
 -f"
 opts=" ${PORTCONF_DEFAULT_OPTS} ${@}"
-grep -q -e " \--yes\>" -e " \-y\>" <<< " ${opts}" && yes="1"
-grep -q -e " \--pretend\>" -e " \-p\>" <<< " ${opts}" && PRETEND="1"
+grep -q -e " --yes\>" -e " -y\>" <<< " ${opts}" && yes="1"
+grep -q -e " --pretend\>" -e " -p\>" <<< " ${opts}" && PRETEND="1"
 opts="$(sed -e 's| --yes\>||g;s| -y\>||g' -e 's| --pretend\>||g;s| -p\>||g' <<< " ${opts}")"
 if grep -q "${eix_dep_keys//\-/\\-}" <<< "${opts}";then
-	if grep -q -e " \--regen-cache\>" -e " \-rc\>" <<< " ${opts}";then
+	if grep -q -e " --regen-cache\>" -e " -rc\>" <<< " ${opts}";then
 		eix_check
 		opts="$(sed -e 's| --regen-cache\>||g;s| -rc\>||g' -e '/^[ \t]$/d' <<< " ${opts}")"
 	else
--- a/portconf	2025-11-28 17:23:26.470689144 +0100
+++ b/portconf	2025-11-28 17:17:52.263919882 +0100
@@ -28,11 +28,52 @@
 ################ ignore ####################################################
 [[ -n "${IGNORE_CATEGORY}" ]] && IGNORE_CATEGORY="$(sed -e '/^$/d' -e 's/$/\/.*/g' <<< "`tr "[:space:]" $'\n' <<< "${IGNORE_CATEGORY}"`")"
 [[ -n "${IGNORE_PN}" ]] && IGNORE_PN="$(sed -e '/^$/d' -e 's/^/.*\//g' <<< "`tr "[:space:]" $'\n' <<< "${IGNORE_PN}"`")"
+
+# Enhanced ignore patterns for directories and files - use config values or defaults
+IGNORE_DIRS="${IGNORE_DIRS:-"package.env env binrepos.conf gnupg"}"
+IGNORE_FILE_PATTERNS="${IGNORE_FILE_PATTERNS:-"zzz_.*"}"
 IGNORE="${IGNORE_CATEGORY}
-${IGNORE_PN}"
+${IGNORE_PN}
+${IGNORE_DIRS}
+${IGNORE_FILE_PATTERNS}"
 IGNORE="$(sed -e '/^$/d' <<< "${IGNORE}")"
 IGNORE="${IGNORE:-'Hello, LOR! :3'}"
 ############################################################################
+################ ignore helper functions ###################################
+should_ignore_path() {
+    local path="$1"
+    
+    # Check if path contains any ignored directory
+    for dir in ${IGNORE_DIRS}; do
+        if [[ "${path}" == *"${dir}"* ]] || [[ "${path}" == *"${dir}/"* ]]; then
+            return 0
+        fi
+    done
+    
+    # Check if filename matches ignore patterns
+    local filename=$(basename "${path}")
+    for pattern in ${IGNORE_FILE_PATTERNS}; do
+        if [[ "${filename}" =~ ${pattern} ]]; then
+            return 0
+        fi
+    done
+    
+    return 1
+}
+
+filter_ignored_paths() {
+	local paths="$1"
+	local filtered=""
+	
+	for path in ${paths}; do
+		if ! should_ignore_path "${path}"; then
+			filtered+=" ${path}"
+		fi
+	done
+	
+	echo "${filtered}"
+}
+############################################################################
 ################ sort_passed_uses ##########################################
 sort_passed_uses(){
 	for opt in ${1};do
@@ -368,6 +409,9 @@
 ################ sort_packages #############################################
 sort_uniq_files(){
 	for package in `find ${PORT_ETC}/ -type f \! -name '*~' \! -name '*.bak' | grep "/package\."`;do
+		# Skip ignored paths
+		should_ignore_path "${package}" && continue
+		
 		tmp_sort="$(mktemp)"
 		echo -e "${underline}Sorting${restore} ${contrast}${package#${PORT_ETC}/}${restore}"
 
@@ -386,15 +430,23 @@
 ############################################################################
 ################ file or dir... ############################################
 file_or_dir(){
-	local founded
-	for i in ${1};do
-		founded+=" $(ls -d1 ${PORT_ETC}/${i} 2>/dev/null)"
-	done
-	if [[ -z "${founded}" ]];then
-		echo -e "${underline}${2}${restore}${contrast}${PORT_ETC}/${1}${restore}: No such file or directory${restore}"
-		eend 1 2>/dev/null
-		return 1
-	fi
+    local founded
+    for i in ${1}; do
+        # Skip ignored patterns
+        should_ignore_path "${PORT_ETC}/${i}" && continue
+        
+        # Check if the path exists before trying to list it
+        if [[ -e "${PORT_ETC}/${i}" ]]; then
+            founded+=" $(ls -d1 ${PORT_ETC}/${i} 2>/dev/null)"
+        fi
+    done
+    founded="$(filter_ignored_paths "${founded}")"
+    
+    if [[ -z "${founded}" ]]; then
+        echo -e "${underline}${2}${restore}${contrast}${PORT_ETC}/${1}${restore}: No such file or directory${restore}"
+        eend 1 2>/dev/null
+        return 1
+  	fi
 	for target in ${founded};do
 		if [[ -f "${target}" ]];then
 			file="${target}"
@@ -408,6 +460,9 @@
 			fi
 		elif [[ -d "${target}" ]];then
 			for f in `find ${target} -type f \! -name '*~' \! -name '*.bak'`;do
+				# Skip ignored files within directories
+				should_ignore_path "${f}" && continue
+				
 				file="${f}"
 				if [[ -s ${file} ]];then
 					echo -e "${underline}${2}${restore} ${contrast}${file#${PORT_ETC}/}${restore}"
@@ -666,6 +721,13 @@
 
 force_not_installed(){
 	for package in `find ${PORT_ETC}/package* -type f \! -name '*~' \! -name '*.bak'`;do
+		# Skip package.env directory entirely
+		if echo "${package}" | grep -q "package\.env"; then
+			continue
+		fi
+		# Skip other ignored paths
+		should_ignore_path "${package}" && continue
+		
 		if [[ -s "${package}" && -n "$(grep -v "^#" < "${package}")" ]];then
 			tmp_package="$(mktemp)"
 			cp "${package}" "${tmp_package}"
@@ -683,6 +745,7 @@
 	done
 
 	for x in `find ${PORT_ETC}/package* -type f`;do
+		should_ignore_path "${x}" && continue
 		if [[ ! -s "${x}" ]];then
 			echo -e "${underline}Empty file${restore} ${contrast}${x}${restore}"
 			remove_ask "${x}"
@@ -745,7 +808,14 @@
 ################ env not_installed #########################################
 env_not_installed(){
 	echo -e "${underline}Looking not installed in${restore} ${contrast}${PORT_ETC}/env${restore}"
+	
+	# Skip if the directory matches ignore patterns
+	should_ignore_path "${PORT_ETC}/env" && return 0
+	
 	for x in "env" "env.d";do
+		# Skip ignored directories
+		should_ignore_path "${PORT_ETC}/${x}" && continue
+		
 		files="$(find ${PORT_ETC}/${x}/ -mindepth 2 -maxdepth 2 -type f \! -name '*~' \! -name '*.bak' 2>/dev/null| cut -d\/ -f5-)"
 		[[ -n "${IGNORE}" ]] && files="$(grep -v "${IGNORE}" <<< "${files}")"
 		dirs="$(find ${PORT_ETC}/${x}/ -type d 2>/dev/null)"
@@ -808,171 +878,195 @@
 ############################################################################
 ################ incorrect uses ############################################
 invalid_uses(){
-	set -f
-	FULL="${PROFILE} ${MAKE_USES}"
-	for opt in ${FULL};do
-		GLOBAL+=" $(echo ${FULL} | tr "[:space:]" $'\n' | grep -e "^${opt#-}$" -e "^-${opt#-}$" | tail -n1)"
-	done
-	GLOBAL="$(echo ${GLOBAL} | tr "[:space:]" $'\n' | sort -u)"
-############################################################################
-	check_uses(){
-		echo -e "${underline}Checking use flags in${restore} ${contrast}${file#${PORT_ETC}/}${restore}:"
-		##### eix env #####
-		export OVERLAYS_LIST="no"
-		export FORMAT='<availableversions:USEONLY>'
-		export USEONLY=' <colliuse>'
-		#### just count
-		tput sc
-		tput civis
-		while read category pn ver slot;do
-			tput el
-			tput el1
-			echo -ne "["; printf "% ${chars}d" $((count--));echo -ne " ]" "atoms left" 2>/dev/null
-			tput rc
-			prepare(){
-				while read string;do
-					struse="${string#${category}/${pn}}"
-					struse="$(tr "[:space:]" $'\n' <<< ${struse})"
-					usefxd="$(sed -e "s|^${trash#-}$||" -e "s|^\-${trash#-}$||" -e '/^$/d' <<< "${struse}")"
-					usefxd="$(tr $'\n' " " <<< "${usefxd}")"
-					usefxd="$(sed -e 's| - | |g' -e 's/[ -]*$//' <<< ${usefxd})"
-					strfxd="${category}/${pn} ${usefxd}"
-					sed -e "s|^${category}/${pn}[[:space:]].*${trash#-}.*|$strfxd|" -i ${tmp_file} 2>/dev/null
-					eend $? 2>/dev/null
-				done <<< "${strings}"
-			}
-
-			prepare_similar(){
-				while read string;do
-					struse="${string#${category}/${pn}}"
-					struse="$(tr "[:space:]" $'\n' <<< ${struse})"
-					usefxd="$(sed -e "s|^${use#-}$|${similar_use}|" -e "s|^\-${use#-}$|\-${similar_use}|" -e '/^$/d' <<< "${struse}")"
-					usefxd="$(tr $'\n' " " <<< "${usefxd}")"
-					usefxd="$(sed -e 's| - | |g' -e 's/[ -]*$//' <<< ${usefxd})"
-					strfxd="${category}/${pn} ${usefxd}"
-					sed -e "s|^${category}/${pn}[[:space:]].*${use#-}.*|$strfxd|" -i ${tmp_file} 2>/dev/null
-					eend $? 2>/dev/null
-				done <<< "${strings}"
-			}
-
-			ALL_USE=" $(eix -e "${category}/${pn}")" || continue
-			ALL_USE="$(sed -e 's| +| |g;s| -| |g;s|(+)||g;s|(-)||g' <<< "${ALL_USE}" | tr "[:space:]" $'\n' | sort -u | sed -e '/^$/d')"
-			LOCAL="$(grep "\<${category}/${pn}\> " "${file}" | cut -d" " -f2- | sed -e "s|#.*||g" | tr "[:space:]" $'\n' | sort -u)"
-			USES="$(sed -e 's|^-||g' <<< "${LOCAL}")"
-			for use in ${USES};do
-				if ! grep -q "^${use}$" <<< "${ALL_USE}" && [[ "${use}" != "*" ]];then
-					for agrep_opt in 1 2 3 B;do
-						for use_opt in "${use}" "^${use}" "${use}$" "^${use}$";do
-							similar_use="$(agrep -${agrep_opt} "${use_opt}" 2>/dev/null <<< "${ALL_USE}")"
-							[[ -n "${similar_use}" ]] && (( $(wc -l <<< "${similar_use}") '==' 1 )) && break
-						done
-						[[ -n "${similar_use}" ]] && (( $(wc -l <<< "${similar_use}") '==' 1 )) && break
-						[[ -z "${similar_use}" ]] || (( $(wc -l <<< "${similar_use}") '>' 1 )) && similar_use=""
-					done
-					if [[ -z "${similar_use}" ]];then
-						grep -q " ${use}\>" <<< "${incorrect_use}" || incorrect_use="${incorrect_use} ${use}"
-					else
-						strings="$(grep "^${category}/${pn}[[:space:]].*\<${use}\>" ${tmp_file})"
-						echo -e "${category}/${pn}: ${red}${use} ---> ${green}${similar_use}${restore}"
-						prepare_similar;
-						incorrect_use="${incorrect_use// ${similar_use}/}"
-					fi
-				else
-					incorrect_use="${incorrect_use// ${use}/}"
-				fi
-
-				if grep -q "^${use}$" <<< "${GLOBAL}" && grep -q "^${use}$" <<< "${LOCAL}";then
-					global_use="${global_use} ${use}"
-				elif grep -q "^-${use}$" <<< "${GLOBAL}" && grep -q "^-${use}$" <<< "${LOCAL}";then
-					global_use="${global_use} -${use}"
-					incorrect_use="${incorrect_use// ${use}/}"
-				fi
-			done
-
-			incorrect_use="$(echo ${incorrect_use} | tr "[:space:]" $'\n' | sed -e 's|  | |g' -e '/^ $/d' -e '/^$/d' | sort -u)"
-			global_use="$(echo ${global_use} | tr "[:space:]" $'\n' | sed -e 's|  | |g' -e '/^ $/d' -e '/^$/d' | sort -u)"
-			if [[ -n "${incorrect_use}" ]];then
-				while read trash;do
-					echo -e "Invalid use: ${green}${category}/${pn}${restore}: ${red}${trash}${restore}"
-					strings="$(grep "^${category}/${pn}[[:space:]].*\<${trash}\>" ${tmp_file})"
-					prepare;
-				done <<< "${incorrect_use}"
-			fi
-			if [[ -n "${global_use}" ]];then
-				while read trash;do
-					echo -e "Global  use: ${green}${category}/${pn}${restore}: ${red}${trash}${restore}"
-					strings="$(grep "^${category}/${pn}[[:space:]].*\<${trash#-}\>" ${tmp_file})"
-					prepare;
-				done <<< "${global_use}"
-			fi
-			unset ALL_USE LOCAL USES incorrect_use global_use use
-		done <<< "`[[ -n "${atoms}" ]] && echo -e "${atoms}"`"
-		while read atom opt;do
-			if [[ -n "${atom}" ]] && [[ -z "${opt}" ]];then
-				echo -e "Removing atom: ${green}${atom}${restore}"
-				sed -e "s|^${atom} *$||" -e '/^$/d' -i "${tmp_file}" 2>/dev/null
-				eend $? 2>/dev/null
-			fi
-		done <<< "$([[ -n "${IGNORE}" ]] && grep -v "${IGNORE}" < "${file}" || cat "${file}")"
-		while read atom opt;do
-			if [[ -n "${atom}" ]] && [[ -z "${opt}" ]];then
-				echo -e "Removing atom: ${green}${atom}${restore}"
-				sed -e "s|^${atom} *$||" -e '/^$/d' -i "${tmp_file}" 2>/dev/null
-				eend $? 2>/dev/null
-			fi
-		done <<< "$([[ -n "${IGNORE}" ]] && grep -v "${IGNORE}" < "${tmp_file}" || cat "${tmp_file}")"
-		eend $? 2>/dev/null
-		unset FORMAT USEONLY
-	}
-	if [[ -f "${PORT_ETC}/package.use" ]];then
-		file="${PORT_ETC}/package.use"
-		tmp_file="$(mktemp)"
-		cp "${file}" "${tmp_file}"
-		if [[ -n "${IGNORE}" ]];then
-			content="$(awk '{print $1}' ${file} | tr -d "<>=~" | sed -e 's|^#.*||g' | grep -v "${IGNORE}")"
-			[[ -n "${content}" ]] && atoms="$(qatom ${content})"
-		else
-			content="$(awk '{print $1}' ${file} | tr -d "<>=~" | sed -e 's|^#.*||g')"
-			[[ -n "${content}" ]] && atoms="$(qatom ${content})"
-		fi
-		count="$(wc -l <<< "${atoms}")"
-		((count--))
-		chars="$(wc -m <<< "${count}")"
-		check_uses;
-		tput el;
-		tput cnorm;
-		diff_ask "${file}" "${tmp_file}"
-		[[ ! -s "${file}" ]] && remove_ask "${file}"
-	elif [[ -d "${PORT_ETC}/package.use" ]];then
-		for f in `find ${PORT_ETC}/package.use/ -type f \! -name '*~' \! -name '*.bak'`;do
-			if [[ -s "${f}" ]];then
-				file="${f}"
-				tmp_file="$(mktemp)"
-				cp "${file}" "${tmp_file}"
-				if [[ -n "${IGNORE}" ]];then
-					content="$(awk '{print $1}' ${file} | tr -d "<>=~" | sed -e 's|^#.*||g' | grep -v "${IGNORE}")"
-					[[ -n "${content}" ]] && atoms="$(qatom ${content})"
-				else
-					content="$(awk '{print $1}' ${file} | tr -d "<>=~" | sed -e 's|^#.*||g')"
-					[[ -n "${content}" ]] && atoms="$(qatom ${content})"
-				fi
-				count="$(wc -l <<< "${atoms}")"
-				((count--))
-				chars="$(wc -m <<< "${count}")"
-				check_uses;
-				tput cnorm
-				diff_ask "${file}" "${tmp_file}"
-				[[ ! -s "${file}" ]] && remove_ask "${file}"
-			else
-				echo -e "${underline}Removing empty file${restore} ${contrast}${f}${restore}"
-				rm ${f} 2>/dev/null
-				eend $? 2>/dev/null
-				continue
-			fi
-		done
-	fi
-	tput cnorm
-	set +f
+    set -f
+    FULL="${PROFILE} ${MAKE_USES}"
+    for opt in ${FULL}; do
+        GLOBAL+=" $(echo ${FULL} | tr "[:space:]" $'\n' | grep -e "^${opt#-}$" -e "^-${opt#-}$" | tail -n1)"
+    done
+    GLOBAL="$(echo ${GLOBAL} | tr "[:space:]" $'\n' | sort -u)"
+############################################################################
+    check_uses(){
+        echo -e "${underline}Checking use flags in${restore} ${contrast}${file#${PORT_ETC}/}${restore}:"
+        ##### eix env #####
+        export OVERLAYS_LIST="no"
+        export FORMAT='<availableversions:USEONLY>'
+        export USEONLY=' <colliuse>'
+        #### just count
+        tput sc
+        tput civis
+        while read category pn ver slot; do
+            tput el
+            tput el1
+            echo -ne "["; printf "% ${chars}d" $((count--)); echo -ne " ]" "atoms left" 2>/dev/null
+            tput rc
+            
+            # Skip if category or package name is null
+            [[ "${category}" == "(null)" || "${pn}" == "(null)" ]] && continue
+
+            prepare(){
+                while read string; do
+                    struse="${string#${category}/${pn}}"
+                    struse="$(tr "[:space:]" $'\n' <<< ${struse})"
+                    usefxd="$(sed -e "s|^${trash#-}$||" -e "s|^\-${trash#-}$||" -e '/^$/d' <<< "${struse}")"
+                    usefxd="$(tr $'\n' " " <<< "${usefxd}")"
+                    usefxd="$(sed -e 's| - | |g' -e 's/[ -]*$//' <<< ${usefxd})"
+                    strfxd="${category}/${pn} ${usefxd}"
+                    sed -e "s|^${category}/${pn}[[:space:]].*${trash#-}.*|$strfxd|" -i ${tmp_file} 2>/dev/null
+                    eend $? 2>/dev/null
+                done <<< "${strings}"
+            }
+
+            prepare_similar(){
+                while read string; do
+                    struse="${string#${category}/${pn}}"
+                    struse="$(tr "[:space:]" $'\n' <<< ${struse})"
+                    usefxd="$(sed -e "s|^${use#-}$|${similar_use}|" -e "s|^\-${use#-}$|\-${similar_use}|" -e '/^$/d' <<< "${struse}")"
+                    usefxd="$(tr $'\n' " " <<< "${usefxd}")"
+                    usefxd="$(sed -e 's| - | |g' -e 's/[ -]*$//' <<< ${usefxd})"
+                    strfxd="${category}/${pn} ${usefxd}"
+                    sed -e "s|^${category}/${pn}[[:space:]].*${use#-}.*|$strfxd|" -i ${tmp_file} 2>/dev/null
+                    eend $? 2>/dev/null
+                done <<< "${strings}"
+            }
+
+            ALL_USE=" $(eix -e "${category}/${pn}")" || continue
+            ALL_USE="$(sed -e 's| +| |g;s| -| |g;s|(+)||g;s|(-)||g' <<< "${ALL_USE}" | tr "[:space:]" $'\n' | sort -u | sed -e '/^$/d')"
+            LOCAL="$(grep "\<${category}/${pn}\> " "${file}" | cut -d" " -f2- | sed -e "s|#.*||g" | tr "[:space:]" $'\n' | sort -u)"
+            USES="$(sed -e 's|^-||g' <<< "${LOCAL}")"
+            
+            for use in ${USES}; do
+                if ! grep -q "^${use}$" <<< "${ALL_USE}" && [[ "${use}" != "*" ]]; then
+                    for agrep_opt in 1 2 3 B; do
+                        for use_opt in "${use}" "^${use}" "${use}$" "^${use}$"; do
+                            similar_use="$(agrep -${agrep_opt} "${use_opt}" 2>/dev/null <<< "${ALL_USE}")"
+                            [[ -n "${similar_use}" ]] && (( $(wc -l <<< "${similar_use}") '==' 1 )) && break
+                        done
+                        [[ -n "${similar_use}" ]] && (( $(wc -l <<< "${similar_use}") '==' 1 )) && break
+                        [[ -z "${similar_use}" ]] || (( $(wc -l <<< "${similar_use}") '>' 1 )) && similar_use=""
+                    done
+                    if [[ -z "${similar_use}" ]]; then
+                        grep -q " ${use}\>" <<< "${incorrect_use}" || incorrect_use="${incorrect_use} ${use}"
+                    else
+                        strings="$(grep "^${category}/${pn}[[:space:]].*\<${use}\>" ${tmp_file})"
+                        echo -e "${category}/${pn}: ${red}${use} ---> ${green}${similar_use}${restore}"
+                        prepare_similar;
+                        incorrect_use="${incorrect_use// ${similar_use}/}"
+                    fi
+                else
+                    incorrect_use="${incorrect_use// ${use}/}"
+                fi
+
+                # FIXED: Only flag as "global use" if it conflicts with make.conf, not profile
+                # Profile USE flags can be overridden per-package, so don't remove them
+                if grep -q "^${use}$" <<< "${MAKE_USES}" && grep -q "^${use}$" <<< "${LOCAL}"; then
+                    echo -e "Make.conf conflict: ${green}${category}/${pn}${restore}: ${red}${use}${restore} (also in make.conf)"
+                    global_use="${global_use} ${use}"
+                elif grep -q "^-${use}$" <<< "${MAKE_USES}" && grep -q "^-${use}$" <<< "${LOCAL}"; then
+                    echo -e "Make.conf conflict: ${green}${category}/${pn}${restore}: ${red}-${use}${restore} (disabled in make.conf)"
+                    global_use="${global_use} -${use}"
+                    incorrect_use="${incorrect_use// ${use}/}"
+                fi
+            done
+
+            incorrect_use="$(echo ${incorrect_use} | tr "[:space:]" $'\n' | sed -e 's|  | |g' -e '/^ $/d' -e '/^$/d' | sort -u)"
+            global_use="$(echo ${global_use} | tr "[:space:]" $'\n' | sed -e 's|  | |g' -e '/^ $/d' -e '/^$/d' | sort -u)"
+            
+            if [[ -n "${incorrect_use}" ]]; then
+                while read trash; do
+                    echo -e "Invalid use: ${green}${category}/${pn}${restore}: ${red}${trash}${restore}"
+                    strings="$(grep "^${category}/${pn}[[:space:]].*\<${trash}\>" ${tmp_file})"
+                    prepare;
+                done <<< "${incorrect_use}"
+            fi
+            
+            # FIXED: Only remove global uses that conflict with make.conf (not profile)
+            if [[ -n "${global_use}" ]]; then
+                while read trash; do
+                    # Only remove if it's a real conflict (both enabled or both disabled)
+                    if [[ "${trash}" != "-"* ]] && grep -q "^${trash}$" <<< "${MAKE_USES}"; then
+                        echo -e "Removing make.conf duplicate: ${green}${category}/${pn}${restore}: ${red}${trash}${restore}"
+                        strings="$(grep "^${category}/${pn}[[:space:]].*\<${trash#-}\>" ${tmp_file})"
+                        prepare;
+                    elif [[ "${trash}" == "-"* ]] && grep -q "^-${trash#-}$" <<< "${MAKE_USES}"; then
+                        echo -e "Removing make.conf duplicate: ${green}${category}/${pn}${restore}: ${red}${trash}${restore}"
+                        strings="$(grep "^${category}/${pn}[[:space:]].*\<${trash#-}\>" ${tmp_file})"
+                        prepare;
+                    fi
+                done <<< "${global_use}"
+            fi
+            
+            unset ALL_USE LOCAL USES incorrect_use global_use use
+        done <<< "`[[ -n "${atoms}" ]] && echo -e "${atoms}"`"
+        
+        while read atom opt; do
+            if [[ -n "${atom}" ]] && [[ -z "${opt}" ]]; then
+                echo -e "Removing atom: ${green}${atom}${restore}"
+                sed -e "s|^${atom} *$||" -e '/^$/d' -i "${tmp_file}" 2>/dev/null
+                eend $? 2>/dev/null
+            fi
+        done <<< "$([[ -n "${IGNORE}" ]] && grep -v "${IGNORE}" < "${file}" || cat "${file}")"
+        
+        while read atom opt; do
+            if [[ -n "${atom}" ]] && [[ -z "${opt}" ]]; then
+                echo -e "Removing atom: ${green}${atom}${restore}"
+                sed -e "s|^${atom} *$||" -e '/^$/d' -i "${tmp_file}" 2>/dev/null
+                eend $? 2>/dev/null
+            fi
+        done <<< "$([[ -n "${IGNORE}" ]] && grep -v "${IGNORE}" < "${tmp_file}" || cat "${tmp_file}")"
+        
+        eend $? 2>/dev/null
+        unset FORMAT USEONLY
+    }
+    
+    if [[ -f "${PORT_ETC}/package.use" ]]; then
+        file="${PORT_ETC}/package.use"
+        tmp_file="$(mktemp)"
+        cp "${file}" "${tmp_file}"
+        if [[ -n "${IGNORE}" ]]; then
+            content="$(awk '{print $1}' ${file} | tr -d "<>=~" | sed -e 's|^#.*||g' | grep -v "${IGNORE}")"
+            [[ -n "${content}" ]] && atoms="$(qatom ${content})"
+        else
+            content="$(awk '{print $1}' ${file} | tr -d "<>=~" | sed -e 's|^#.*||g')"
+            [[ -n "${content}" ]] && atoms="$(qatom ${content})"
+        fi
+        count="$(wc -l <<< "${atoms}")"
+        ((count--))
+        chars="$(wc -m <<< "${count}")"
+        check_uses;
+        tput el;
+        tput cnorm;
+        diff_ask "${file}" "${tmp_file}"
+        [[ ! -s "${file}" ]] && remove_ask "${file}"
+    elif [[ -d "${PORT_ETC}/package.use" ]]; then
+        for f in `find ${PORT_ETC}/package.use/ -type f \! -name '*~' \! -name '*.bak'`; do
+            if [[ -s "${f}" ]]; then
+                file="${f}"
+                tmp_file="$(mktemp)"
+                cp "${file}" "${tmp_file}"
+                if [[ -n "${IGNORE}" ]]; then
+                    content="$(awk '{print $1}' ${file} | tr -d "<>=~" | sed -e 's|^#.*||g' | grep -v "${IGNORE}")"
+                    [[ -n "${content}" ]] && atoms="$(qatom ${content})"
+                else
+                    content="$(awk '{print $1}' ${file} | tr -d "<>=~" | sed -e 's|^#.*||g')"
+                    [[ -n "${content}" ]] && atoms="$(qatom ${content})"
+                fi
+                count="$(wc -l <<< "${atoms}")"
+                ((count--))
+                chars="$(wc -m <<< "${count}")"
+                check_uses;
+                tput cnorm
+                diff_ask "${file}" "${tmp_file}"
+                [[ ! -s "${file}" ]] && remove_ask "${file}"
+            else
+                echo -e "${underline}Removing empty file${restore} ${contrast}${f}${restore}"
+                rm ${f} 2>/dev/null
+                eend $? 2>/dev/null
+                continue
+            fi
+        done
+    fi
+    tput cnorm
+    set +f
 }
 ############################################################################
 ################ incorrect uses in make.conf ###############################
@@ -988,39 +1082,47 @@
 }
 
 invalid_uses_make(){
-	set -f
-	echo -e "${underline}Checking use flags in${restore} ${contrast}${makefile}${restore}"
-	tmp_file="$(mktemp)"
-	cp "${makefile}" "${tmp_file}"
-
-	vars_in_USE="$(make_conf_use USE | hell_parser | grep '\$' | tr -d '${}')"
-	real_uses="$(eix --print-all-useflags | sed 's|^[-+]||g;s|^(+)||g' | sort -u)"
-	for var in ${vars_in_USE} USE;do
-		sub_uses="$(make_conf_use ${var} | hell_parser | grep -v '\$')"
-		for use in ${sub_uses};do
-			if ! grep -q "^${use}$" <<< "${real_uses}" && [[ "${use}" != "*" ]];then
-				echo -ne "Invalid use ${contrast} ${var}: ${red}${use}${restore}" | column -t
-				invalid_uses+=" ${use}"
-			fi
-		done
-	done
-
-	if [[ -n "${invalid_uses}" ]];then
-		for iuse in ${invalid_uses};do
-			line="$(grep "\<${iuse}\>" ${tmp_file})"
-			fixed_line="$(sed "s|[- \t]${iuse}||" <<< "${line}")"
-			sed -e "s|${line%\\}|${fixed_line%\\}|" -i "${tmp_file}"
-		done
-	fi
-	diff_ask "${makefile}" "${tmp_file}"
-	set +f
+    set -f
+    echo -e "${underline}Checking use flags in${restore} ${contrast}${makefile}${restore}"
+    tmp_file="$(mktemp)"
+    cp "${makefile}" "${tmp_file}"
+
+    vars_in_USE="$(make_conf_use USE | hell_parser | grep '\$' | tr -d '${}')"
+    real_uses="$(eix --print-all-useflags | sed 's|^[-+]||g;s|^(+)||g' | sort -u)"
+    
+    for var in ${vars_in_USE} USE; do
+        sub_uses="$(make_conf_use ${var} | hell_parser | grep -v '\$')"
+        for use in ${sub_uses}; do
+            if ! grep -q "^${use}$" <<< "${real_uses}" && [[ "${use}" != "*" ]]; then
+                echo -ne "Invalid use ${contrast} ${var}: ${red}${use}${restore}" | column -t
+                invalid_uses+=" ${use}"
+            fi
+        done
+    done
+
+    if [[ -n "${invalid_uses}" ]]; then
+        for iuse in ${invalid_uses}; do
+            # Use a safer approach to modify the file
+            sed -i "s/\([[:space:]]\)\?${iuse}\([[:space:]]\)\?/ /g" "${tmp_file}"
+            # Clean up multiple spaces
+            sed -i 's/  */ /g' "${tmp_file}"
+            sed -i 's/^ //' "${tmp_file}"
+            sed -i 's/ $//' "${tmp_file}"
+        done
+    fi
+    diff_ask "${makefile}" "${tmp_file}"
+    set +f
 }
+
 ############################################################################
 ################ not_found #################################################
 not_found(){
 	echo -e "${underline}Checking invalid entries${restore}..."
 	TRASH="$(LANG=en eix -Ttc 2>/dev/null)"
 	for package in $(ls -d1 ${PORT_ETC}/package* | grep -v -e "~" -e "\.bak" -e "\.old");do
+		# Skip ignored paths
+		should_ignore_path "${package}" && continue
+		
 		incorrect="$(echo -e "${TRASH}" | tr $'\n' "%" | sed -e "s|.*${package}:||" -e 's|--.*||' -e 's|No.*||'|\
 		tr "%" $'\n' | sed -e '/^$/d' | grep -v "${IGNORE}")"
 		if [[ -n "${incorrect}" && -f "${package}" ]];then
@@ -1068,11 +1170,17 @@
 		INVALID_FOUNDED+="${line}"$'\n'
 
 		if [[ -n "${line}" && -f "${file}" ]];then
+			# Skip ignored files
+			should_ignore_path "${file}" && continue
+			
 			tmp_file="$(mktemp)"
 			cp "${file}" "${tmp_file}"
 			[[ -n "${line}" ]] && sed -e "s|`echo $line`$||" -e 's|[ \t]| |' -e '/^[ \t]$/d' -e '/^$/d' -i ${tmp_file}
 			diff_ask "${file}" "${tmp_file}"
 		elif [[ -n "${line}" && -d "${file}" ]];then
+			# Skip ignored directories
+			should_ignore_path "${file}" && continue
+			
 			for package in `grep -RH "${line//'*'/\*}" "${file}"/ | awk -F \: '{print $1}'`;do
 					tmp_package="$(mktemp)"
 					cp "${package}" "${tmp_package}"
@@ -1140,6 +1248,8 @@
 empty_files(){
 	echo -e "${underline}Looking empty files${restore}"
 	for target in `find ${PORT_ETC} -type f`;do
+		# Skip ignored paths
+		should_ignore_path "${target}" && continue
 		[[ ! -s "${target}" || -z "$(grep -v "^#" < "${target}")" ]] && remove_ask "${target}"
 	done
 	eend 0 2>/dev/null
@@ -1149,6 +1259,8 @@
 backup_files(){
 	echo -e "${underline}Looking backup files${restore}"
 	for target in `find ${PORT_ETC} -type f \( -name "*~" -o  -name "*.bak" -o -name "*.old" \)`;do
+		# Skip ignored paths
+		should_ignore_path "${target}" && continue
 		remove_ask "${target}"
 	done
 	eend 0 2>/dev/null
@@ -1156,7 +1268,10 @@
 ############################################################################
 ################ package.* files 2 dirs ####################################
 f_to_d(){
-	while read package;do
+	while read package; do
+		# Skip ignored paths
+		should_ignore_path "${package}" && continue
+		
 		if [[ -f "${package}" ]];then
 			echo -e "${underline}Processing${restore}: ${contrast}${package##*/}${restore}"
 			tmp_file="$(mktemp)"
@@ -1164,7 +1279,7 @@
 			sed -e 's|^#.*||g' -i "${tmp_file}"
 			dir="${PORT_ETC}/${package##*/}"
 			mkdir "${dir}"
-			while read line;do
+			while read line; do
 			set -f
 				atom="$(awk '{print $1}' <<< "${line}")"
 				category="$(awk '{print $1}' <<< `qatom ${atom}`)"
@@ -1186,7 +1301,10 @@
 ############################################################################
 ################ package.* dirs 2 files ####################################
 d_to_f(){
-	while read package;do
+	while read package; do
+		# Skip ignored paths
+		should_ignore_path "${package}" && continue
+		
 		if [[ -d "${package}" ]];then
 			echo -e "${underline}Processing${restore}: ${contrast}${package##*/}${restore}"
 			tmp_file="$(mktemp)"
@@ -1384,6 +1502,9 @@
 sort_uniq_mask_use(){
 	if [[ -d "${PORT_ETC}/profile" || -h "${PORT_ETC}/profile" ]];then
 		for package in `find ${PORT_ETC}/profile -type f \! -name '*~' \! -name '*.bak' -name "use.stable.mask" -or -name "use.mask"`;do
+			# Skip ignored paths
+			should_ignore_path "${package}" && continue
+			
 			tmp_sort="$(mktemp)"
 			echo -e "${underline}Sorting${restore} ${contrast}${package#${PORT_ETC}/}${restore}"
 
@@ -1454,9 +1575,14 @@
 }
 
 check_use_masked() {
-	for target in $(mask_files);do
-		file_or_dir "profile/${target}" "Checking masked uses:" "etc_profile_use_mask" || return 1
-	done
+    for target in $(mask_files); do
+        # Check if the target exists before processing
+        if [[ -e "${PORT_ETC}/profile/${target}" ]] || [[ -d "${PORT_ETC}/profile/${target}" ]]; then
+            file_or_dir "profile/${target}" "Checking masked uses:" "etc_profile_use_mask" || continue
+        else
+            echo -e "${underline}Skipping${restore} ${contrast}profile/${target}${restore}: does not exist"
+        fi
+    done
 }
 ############################################################################
 ################ regen_world ###############################################
@@ -1559,15 +1685,21 @@
 ############################################################################
 ################ unused repo and dep-cache #################################
 overlays(){
-	########## repo over layman
-	layman_path="$(awk '/storage[[:space:]].*:/ {print $3}' /etc/layman/layman.cfg)"
-	source "${layman_path}/make.conf" 2>/dev/null
-	layman_pkgdir="$(tr '[[:space:]]' $'\n' <<< "${PORTDIR_OVERLAY}" | sed '/^$/d')"
-	for repo_dir in ${layman_pkgdir};do
-		[[ -f "${repo_dir}/profiles/repo_name" ]] && repo_name="$(cat "${repo_dir}/profiles/repo_name")"
-		repo_name="${repo_name:-${repo_dir##*/}}"
-		layman_overlays+="${repo_dir} ${repo_name}"$'\n'
-	done
+    ########## repo over layman
+    local layman_path=""
+    if [[ -f "/etc/layman/layman.cfg" ]]; then
+        layman_path="$(awk '/storage[[:space:]].*:/ {print $3}' /etc/layman/layman.cfg 2>/dev/null)"
+    fi
+    
+    if [[ -n "${layman_path}" && -f "${layman_path}/make.conf" ]]; then
+        source "${layman_path}/make.conf" 2>/dev/null
+        layman_pkgdir="$(tr '[[:space:]]' $'\n' <<< "${PORTDIR_OVERLAY}" | sed '/^$/d')"
+        for repo_dir in ${layman_pkgdir}; do
+            [[ -f "${repo_dir}/profiles/repo_name" ]] && repo_name="$(cat "${repo_dir}/profiles/repo_name")"
+            repo_name="${repo_name:-${repo_dir##*/}}"
+            layman_overlays+="${repo_dir} ${repo_name}"$'\n'
+        done
+    fi
 
 	all_overlays="${layman_overlays}"
 
--- a/portconf.conf	2025-11-28 17:23:04.735509754 +0100
+++ b/portconf.conf	2025-11-28 17:16:38.034301543 +0100
@@ -8,5 +8,11 @@
 #dont check following packages names
 #IGNORE_PN=""
 
+# Directories to ignore in /etc/portage/
+IGNORE_DIRS="package.env env binrepos.conf gnupg profile"
+
+# File patterns to ignore
+IGNORE_FILE_PATTERNS="zzz.*"
+
 #default options. '-rc' Highly recommend!
 PORTCONF_DEFAULT_OPTS="-rc"
--- a/portconf	2025-11-28 18:05:40.357013362 +0100
+++ b/portconf	2025-11-28 18:19:52.265525061 +0100
@@ -657,101 +657,107 @@
 ############################################################################
 ################ not_installed #############################################
 installed(){
-	installed="$(qlist -ICSec "${category}/${pn}" | awk '{print $2}')"
-	if [[ -n "${installed}" ]];then
-		installed_vers="$(awk -F \: '{print $1}' <<< "${installed}")"
-		installed_min_ver="$(head -n1 <<< "${installed_vers}")"
-		installed_max_ver="$(tail -n1 <<< "`grep -v 9999 <<< "${installed_vers}"`")"
-		installed_live_ver="$(tail -n1 <<< "`grep 9999 <<< "${installed_vers}"`")"
-		installed_slots="$(awk -F \: '{print $2}' <<< "${installed}")"
-		#::repo check
-		full_vers="$(qlist -ICev "${category}/${pn}" | sed "s|${category}/${pn}-||g")"
-		(( "$(wc -l <<< "${full_vers}")" '>' "1" ))
-		if [[ -n "${defined_repo}" ]];then
-			for ver in ${full_vers};do
-				all_vers+=" ${PKGDB}/${category}/${pn}-${ver}/repository"
-			done
-			grep -qe "^${defined_repo}$" ${all_vers} || unset installed
-			unset all_vers
-		fi
-		[[ "${installed_slots}" == "0" ]] && unset installed_slots
-	fi
+    installed="$(qlist -ICSec "${category}/${pn}" | awk '{print $2}')"
+    if [[ -n "${installed}" ]]; then
+        installed_vers="$(awk -F \: '{print $1}' <<< "${installed}")"
+        installed_min_ver="$(head -n1 <<< "${installed_vers}")"
+        installed_max_ver="$(tail -n1 <<< "`grep -v 9999 <<< "${installed_vers}"`")"
+        installed_live_ver="$(tail -n1 <<< "`grep 9999 <<< "${installed_vers}"`")"
+        installed_slots="$(awk -F \: '{print $2}' <<< "${installed}")"
+        #::repo check
+        full_vers="$(qlist -ICev "${category}/${pn}" | sed "s|${category}/${pn}-||g")"
+        
+        # FIXED: Get line count without whitespace
+        line_count=$(wc -l <<< "${full_vers}" | tr -d '[:space:]')
+        
+        # FIXED: Use numeric comparison without quotes
+        if (( line_count > 1 )); then
+            if [[ -n "${defined_repo}" ]]; then
+                for ver in ${full_vers}; do
+                    all_vers+=" ${PKGDB}/${category}/${pn}-${ver}/repository"
+                done
+                grep -qe "^${defined_repo}$" ${all_vers} || unset installed
+                unset all_vers
+            fi
+        fi
+        [[ "${installed_slots}" == "0" ]] && unset installed_slots
+    fi
 }
 
 not_if(){
-	atoms="$(awk '{print $1}' <<< "`grep -v "^#" < ${package}`")"
-	[[ -n "${IGNORE}" ]] && atoms="$(grep -v "${IGNORE}" <<< "${atoms}")"
-	echo -e "${underline}Checking${restore} ${contrast}$package${restore}"
-	if [[ -n "${atoms}" ]];then
-		while read atom;do
-			#::repo check
-			if grep -q "::" <<< "${atom}";then
-				defined_repo="${atom##*::}"
-			else
-				unset defined_repo
-			fi
-			[[ -n "${defined_repo}" ]] && atom="${atom%%::${defined_repo}}"
-			while read category pn ver rev slot;do
-				sw="$(grep -o "[<>=~]" <<< "${category}" | tr -d $'\n')"
-				category="${category##${sw}}"
-
-				[[ "${category}" == "(null)" || "${pn}" == "(null)" ]] && continue
-
-				if [[ -n "${rev}" ]] && [[ -z "${slot}" ]] && `grep -q \: <<< "${rev}"`;then
-					slot="${rev}"
-					unset rev
-				fi
-				slot="${slot#:}"
-				pn="${pn%:}"
-				installed;
-
-				if [[ -z "${installed}" ]];then
-					if [[ -n "${defined_repo}" ]];then
-						echo -e "${red}Not installed${restore} ${green}${category}/${pn}::${underline}${defined_repo}${restore}"
-					else
-						echo -e "${red}Not installed${restore} ${green}${category}/${pn}${restore}"
-					fi
-					sed -e "s|.*\<${category}/${pn}\>.*||" -e '/^$/d' -i "${tmp_package}" 2>/dev/null
-					eend $? 2>/dev/null
-				fi
-			done <<< `qatom "${atom}"`
-		done <<< "${atoms}"
-	fi
+    atoms="$(awk '{print $1}' <<< "`grep -v "^#" < ${package}`")"
+    [[ -n "${IGNORE}" ]] && atoms="$(grep -v "${IGNORE}" <<< "${atoms}")"
+    echo -e "${underline}Checking${restore} ${contrast}$package${restore}"
+    if [[ -n "${atoms}" ]]; then
+        while read atom; do
+            #::repo check
+            if grep -q "::" <<< "${atom}"; then
+                defined_repo="${atom##*::}"
+            else
+                unset defined_repo
+            fi
+            [[ -n "${defined_repo}" ]] && atom="${atom%%::${defined_repo}}"
+            while read category pn ver rev slot; do
+                sw="$(grep -o "[<>=~]" <<< "${category}" | tr -d $'\n')"
+                category="${category##${sw}}"
+
+                [[ "${category}" == "(null)" || "${pn}" == "(null)" ]] && continue
+
+                if [[ -n "${rev}" ]] && [[ -z "${slot}" ]] && `grep -q \: <<< "${rev}"`; then
+                    slot="${rev}"
+                    unset rev
+                fi
+                slot="${slot#:}"
+                pn="${pn%:}"
+                installed;
+
+                if [[ -z "${installed}" ]]; then
+                    if [[ -n "${defined_repo}" ]]; then
+                        echo -e "${red}Not installed${restore} ${green}${category}/${pn}::${underline}${defined_repo}${restore}"
+                    else
+                        echo -e "${red}Not installed${restore} ${green}${category}/${pn}${restore}"
+                    fi
+                    sed -e "s|.*\<${category}/${pn}\>.*||" -e '/^$/d' -i "${tmp_package}" 2>/dev/null
+                    eend $? 2>/dev/null
+                fi
+            done <<< `qatom "${atom}"`
+        done <<< "${atoms}"
+    fi
 }
 
 force_not_installed(){
-	for package in `find ${PORT_ETC}/package* -type f \! -name '*~' \! -name '*.bak'`;do
-		# Skip package.env directory entirely
-		if echo "${package}" | grep -q "package\.env"; then
-			continue
-		fi
-		# Skip other ignored paths
-		should_ignore_path "${package}" && continue
-		
-		if [[ -s "${package}" && -n "$(grep -v "^#" < "${package}")" ]];then
-			tmp_package="$(mktemp)"
-			cp "${package}" "${tmp_package}"
-			if ! `grep -q "\.mask" <<< "${package}"`;then
-				not_if;
-				eend $? 2>/dev/null
-			fi
-			diff_ask "${package}" "${tmp_package}"
-		else
-			pack="${package%/*}"
-			echo -e "${underline}Empty file${restore} ${contrast}${pack}${restore}"
-			remove_ask "${package}"
-			eend $? 2>/dev/null
-		fi
-	done
-
-	for x in `find ${PORT_ETC}/package* -type f`;do
-		should_ignore_path "${x}" && continue
-		if [[ ! -s "${x}" ]];then
-			echo -e "${underline}Empty file${restore} ${contrast}${x}${restore}"
-			remove_ask "${x}"
-			eend $? 2>/dev/null
-		fi
-	done
+    for package in `find ${PORT_ETC}/package* -type f \! -name '*~' \! -name '*.bak'`; do
+        # Skip package.env directory entirely
+        if echo "${package}" | grep -q "package\.env"; then
+            continue
+        fi
+        # Skip other ignored paths
+        should_ignore_path "${package}" && continue
+        
+        if [[ -s "${package}" && -n "$(grep -v "^#" < "${package}")" ]]; then
+            tmp_package="$(mktemp)"
+            cp "${package}" "${tmp_package}"
+            if ! `grep -q "\.mask" <<< "${package}"`; then
+                not_if;
+                eend $? 2>/dev/null
+            fi
+            diff_ask "${package}" "${tmp_package}"
+        else
+            pack="${package%/*}"
+            echo -e "${underline}Empty file${restore} ${contrast}${pack}${restore}"
+            remove_ask "${package}"
+            eend $? 2>/dev/null
+        fi
+    done
+
+    for x in `find ${PORT_ETC}/package* -type f`; do
+        should_ignore_path "${x}" && continue
+        if [[ ! -s "${x}" ]]; then
+            echo -e "${underline}Empty file${restore} ${contrast}${x}${restore}"
+            remove_ask "${x}"
+            eend $? 2>/dev/null
+        fi
+    done
 }
 ############################################################################
 ################ package.env conf ##########################################