Hi, I wrote emails and a bugreport for this issue but never got an answer...

Currently eetckeeper does ignore the .hgignore file. My workflow is like this:
I have a hgignore to ignore everything and adding files explicitly. There are also exceptions from that where I want to track for new files:

Ignoring everyhing would be:
    
    syntax: glob
    **

With exceptions:

    syntax: regexp

    # Ignore anything in root folder but include .hgignore and special folders:
    #^(?!.hgignore|data|DATA|NFS|usr(/local(/lib(/site_perl|$)|$)|$)|etc(/init.d(/*.sh$|$)|$))
    # OR
    ^(?!boot(/config|$)|etc(/runlevels|$))

The long time problem is that etckeeper tries to scan the whole repo root which is / here because I also track some items in /usr/local or /root. Those find on / take far too long and never come back.

Therefore I dropped pre-commit.d/20warn-problem-files completely since I know which files I added explicitly. I also dropped the search for empty directories because I only add specific files.
As for 30store-metadata I added hg status -nacu for getting all relevant files:

[[!format  bash """
--- /root/src/etckeeper/pre-commit.d/30store-metadata	2015-02-19 13:13:46.171485949 +0100
+++ pre-commit.d/30store-metadata	2015-02-19 13:28:01.593456235 +0100
@@ -59,7 +59,10 @@ generate_metadata() {
 	# (Note that when using this, the find expression must end with 
 	# -print or -exec, else the excluded directories will actually be
 	# printed!)
-	NOVCS='. -path ./.git -prune -o -path ./.bzr -prune -o -path ./.hg -prune -o -path ./_darcs -prune -o'
+	if [ "$VCS" = hg ]; then
+            HG_FILES="$(hg status -nacu)"
+        fi
+	NOVCS="${HG_FILES:-.} -path ./.git -prune -o -path ./.bzr -prune -o -path ./.hg -prune -o -path ./_darcs -prune -o"
 
 	# Keep the sort order the same at all times.
 	LC_COLLATE=C
@@ -68,8 +71,9 @@ generate_metadata() {
 	if [ "$VCS" = git ] || [ "$VCS" = hg ]; then
 		# These version control systems do not track directories,
 		# so empty directories must be stored specially.
-		find $NOVCS -type d -empty -print |
-			sort | shellquote | sed -e "s/^/mkdir -p /"
+#		find ${HG_FILES:- } $NOVCS -type d -empty -print |
+#			sort | shellquote | sed -e "s/^/mkdir -p /"
+                true
 	fi
 
 	if [ "$VCS" = darcs ]; then
@@ -110,12 +114,12 @@ generate_metadata() {
 		s/^/$q/;
 		s/$/$q/;
 		if ($uid != $>) {
-			printf "maybe chown $q%s$q %s\n", uidname($uid), $_;
+			printf "maybe chown -c $q%s$q %s\n", uidname($uid), $_;
 		}
 		if ($gid != $)) {
-			printf "maybe chgrp $q%s$q %s\n", gidname($gid), $_;
+			printf "maybe chgrp -c $q%s$q %s\n", gidname($gid), $_;
 		}
-		printf "maybe chmod %04o %s\n", $mode & 07777, $_;
+		printf "maybe chmod -c %04o %s\n", $mode & 07777, $_;
 	'
"""]]

Thanks for the new website beside the very basic debian bugtracker. Please provide a bug tracker or ticket system. Please provide also simple tar-balls with the release-versions beside git-tags, that can be used by other package managers and distributions.

Since some distros are already considered please integrate the Gentoo package manager so we can drop our patches:

<http://sources.gentoo.org/cgi-bin/viewvc.cgi/gentoo-x86/sys-apps/etckeeper/files/etckeeper-1.15-gentoo.patch>

# There is something missing if only recording uid/gid/mode for tracked files...
All dirnames of every file must also get the right permissions.

I only did the hg source part. Using bash arrays could be better, I tried to stay sh compatible. This is a quick hack, not completely tested...

[[!format  bash """
# diff -uNr /root/src/etckeeper/pre-commit.d/30store-metadata /etc/etckeeper/pre-commit.d/30store-metadata 
--- /root/src/etckeeper/pre-commit.d/30store-metadata	2015-02-20 15:36:24.912374338 +0100
+++ /etc/etckeeper/pre-commit.d/30store-metadata	2015-02-20 15:34:10.770378997 +0100
@@ -44,6 +44,21 @@
 	sed -e "s/'/'\"'\"'/g" -e "s/^/'/" -e "s/$/'/"
 }
 
+getdirname() {
+    # Permissions of all parent dirnames must also be recorded
+    local p
+    # Print the file itself
+    printf '%s' "$p"
+    p=${1%/*}
+    #  Print the files dirnames
+    while [[ $p = */* ]]; do
+        printf ' %s' "$p"
+        p=${p%/*}
+    done
+    #  Print the parent dirname
+    printf ' %s' "$p"
+}
+
 generate_metadata() {
 	# This function generates the script commands to fix any file
 	# ownerships that aren't owner=root, group=root, as well as to 
@@ -57,9 +72,17 @@
 	# but we want find to ignore the VCS files themselves.
 	# 
 	# (Note that when using this, the find expression must end with 
-	# -print or -exec, else the excluded directories will actually be
-	# printed!)
-	NOVCS='. -path ./.git -prune -o -path ./.bzr -prune -o -path ./.hg -prune -o -path ./_darcs -prune -o'
+        # -print or -exec, else the excluded directories will actually be
+        # printed!)
+        if [ "$VCS" = hg ]; then
+            HG_FILES="$(hg status -nacu)"
+            HG_FILES_DIRS=""
+            for file in $HG_FILES; do
+                HG_FILES_DIRS+=" $(getdirname $file)"
+            done
+
+        fi
+	NOVCS="${ALL_FILES:-.} -path ./.git -prune -o -path ./.bzr -prune -o -path ./.hg -prune -o -path ./_darcs -prune -o"
 
 	# Keep the sort order the same at all times.
 	LC_COLLATE=C
@@ -68,8 +91,9 @@
 	if [ "$VCS" = git ] || [ "$VCS" = hg ]; then
 		# These version control systems do not track directories,
 		# so empty directories must be stored specially.
-		find $NOVCS -type d -empty -print |
-			sort | shellquote | sed -e "s/^/mkdir -p /"
+#		find ${ALL_FILES:- } $NOVCS -type d -empty -print |
+#			sort | shellquote | sed -e "s/^/mkdir -p /"
+                true
 	fi
 
 	if [ "$VCS" = darcs ]; then
@@ -83,7 +107,8 @@
  
 	# Store things that don't have the default user or group.
 	# Store all file modes, in case the user has an unusual umask.
-	find $NOVCS \( -type f -or -type d \) -print | filter_ignore | sort | perl -ne '
+	#find $NOVCS \( -type f -or -type d \) -print | filter_ignore | sort | perl -ne '
+	echo $HG_FILES_DIRS | tr " " "\n" | sort -u | perl -ne '
 		BEGIN { $q=chr(39) }
 		sub uidname {
 			my $want=shift;
@@ -110,12 +135,12 @@
 		s/^/$q/;
 		s/$/$q/;
 		if ($uid != $>) {
-			printf "maybe chown $q%s$q %s\n", uidname($uid), $_;
+			printf "maybe chown -c $q%s$q %s\n", uidname($uid), $_;
 		}
 		if ($gid != $)) {
-			printf "maybe chgrp $q%s$q %s\n", gidname($gid), $_;
+			printf "maybe chgrp -c $q%s$q %s\n", gidname($gid), $_;
 		}
-		printf "maybe chmod %04o %s\n", $mode & 07777, $_;
+		printf "maybe chmod -c %04o %s\n", $mode & 07777, $_;
 	'
 
 	# We don't handle xattrs.
"""]]

I added an init hook for any update, so after cloning to a new location and updating, all permissions are going to be fixed:
[hooks]

[[!format python """
# pre-commit hook for etckeeper, to store metadata and do sanity checks
pre-commit	= etckeeper pre-commit -d "$(hg root)"
post-update	= etckeeper init "$(hg root)"
"""]]

Best regards,
Massimo
