I came across a similar issue while trying to convert the package ufraw to
use dh-autoreconf.
At the start of the second build, dh_autoreconf_clean would delete
mkinstalldirs and the build would fail.
It seems that dh_autoreconf was replacing mkinstalldirs with a copy from
/usr/share/automake-1.11/mkinstalldirs, and there were minor differences
between these two files, causing dh_autoreconf_clean to delete the modified
file.
For now, I have patched mkinstalldirs included with ufraw as below, but
this seems a rather fragile workaround.
--- a/mkinstalldirs
+++ b/mkinstalldirs
@@ -81,9 +81,9 @@
echo "mkdir -p -- $*"
exec mkdir -p -- "$@"
else
- # On NextStep and OpenStep, the 'mkdir' command does not
+ # On NextStep and OpenStep, the `mkdir' command does not
# recognize any option. It will interpret all options as
- # directories to create, and then abort because '.' already
+ # directories to create, and then abort because `.' already
# exists.
test -d ./-p && rmdir ./-p
test -d ./--version && rmdir ./--version
