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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, $_;
 	'
"""]]