deploy: Copy parent directories for modified config files

Previously, in the case where a parent directory of a modified config
file was removed, we would throw an exception.  This happens when
switching from a tree that has some software (e.g. firewalld), to one
that does not.

While it's nice to have this warning that your config file probably no
longer applies, there's no need to make it so...fatal.

It's particularly problematic that the only easy workaround is to
remove the config files from your current tree - which breaks
rollback.

The solution then is for for us to take ownership of the parent
directories too into the new /etc.  Admins can clean up these files
afterwards at any time.

https://bugzilla.gnome.org/show_bug.cgi?id=734293

tests/test-admin-deploy-etcmerge-cornercases.sh

@@ -37,8 +37,12 @@ echo "rev=${rev}"
 ostree admin --sysroot=sysroot deploy --karg=root=LABEL=MOO --karg=quiet --os=testos testos:testos/buildmaster/x86_64-runtime
 assert_has_dir sysroot/boot/ostree/testos-${bootcsum}
 
-# Ok, let's create a long directory chain with custom permissions
 etc=sysroot/ostree/deploy/testos/deploy/${rev}.0/etc
+
+# modified config file
+echo "a modified config file" > ${etc}/NetworkManager/nm.conf
+
+# Ok, let's create a long directory chain with custom permissions
 mkdir -p ${etc}/a/long/dir/chain
 mkdir -p ${etc}/a/long/dir/forking
 chmod 700 ${etc}/a
@@ -47,14 +51,24 @@ chmod 777 ${etc}/a/long/dir
 chmod 707 ${etc}/a/long/dir/chain
 chmod 700 ${etc}/a/long/dir/forking
 
+# Symlink to nonexistent path, to ensure we aren't walking symlinks
+ln -s no-such-file ${etc}/a/link-to-no-such-file
+
+# Remove a directory
+rm ${etc}/testdirectory -rf
+
 # Now deploy a new commit
 os_repository_new_commit
 ostree --repo=sysroot/ostree/repo remote add --set=gpg-verify=false testos file://$(pwd)/testos-repo testos/buildmaster/x86_64-runtime
 ostree admin --sysroot=sysroot upgrade --os=testos
 newrev=$(ostree --repo=sysroot/ostree/repo rev-parse testos/buildmaster/x86_64-runtime)
 echo "newrev=${newrev}"
+newroot=sysroot/ostree/deploy/testos/deploy/${newrev}.0
+newetc=${newroot}/etc
+
+assert_file_has_content ${newroot}/usr/etc/NetworkManager/nm.conf "a default daemon file"
+assert_file_has_content ${newetc}/NetworkManager/nm.conf "a modified config file"
 
-newetc=sysroot/ostree/deploy/testos/deploy/${newrev}.0/etc
 assert_file_has_mode() {
   stat -c '%a' $1 > mode.txt
   if ! grep -q -e "$2" mode.txt; then 
@@ -63,6 +77,7 @@ assert_file_has_mode() {
   fi
   rm -f mode.txt
 }
+
 assert_file_has_mode ${newetc}/a 700
 assert_file_has_mode ${newetc}/a/long 770
 assert_file_has_mode ${newetc}/a/long/dir 777
@@ -70,6 +85,11 @@ assert_file_has_mode ${newetc}/a/long/dir/chain 707
 assert_file_has_mode ${newetc}/a/long/dir/forking 700
 assert_file_has_mode ${newetc}/a/long/dir 777
 
+test -L ${newetc}/a/link-to-no-such-file || assert_not_reached "should have symlink"
+
+assert_has_dir ${newroot}/usr/etc/testdirectory
+assert_not_has_dir ${newetc}/testdirectory
+
 echo "ok"
 
 # Add /etc/initially-empty
@@ -116,10 +136,10 @@ ostree --repo=${test_tmpdir}/testos-repo commit -b testos/buildmaster/x86_64-run
 cd ${test_tmpdir}
 newconfpath=sysroot/ostree/deploy/testos/deploy/${rev}.0/etc/initially-empty/mynewfile
 touch ${newconfpath}
-if ostree admin --sysroot=sysroot upgrade --os=testos 2>err.txt; then
-    assert_not_reached "upgrade should have failed"
-fi
-assert_file_has_content err.txt "New tree removes parent directory"
+ostree admin --sysroot=sysroot upgrade --os=testos
+rev=$(ostree --repo=sysroot/ostree/repo rev-parse testos/buildmaster/x86_64-runtime)
+assert_not_has_file sysroot/ostree/deploy/testos/deploy/${rev}.0/usr/etc/initially-empty
+assert_has_file sysroot/ostree/deploy/testos/deploy/${rev}.0/etc/initially-empty/mynewfile
 rm ${newconfpath}
 
 echo "ok"