Ben's got some scripts for those...include/libmesh/rebuild_makefile.sh for include/libmesh/Makefile.am
include/rebuild_include_HEADERS.sh for include/include_HEADERS
src/rebuild_libmesh_SOURCES.sh for src/libmesh_SOURCES
Hey, Ben: should we be just running those scripts automatically from
bootstrap? It's annoying that automake can't figure out targets based
on filesystem globbing and string pattern substitutions like your
scripts do... but we never actually run automake directly, we just run
bootstrap, which is a shell script that can run other shell scripts
which can all glob to their hearts' content.
ding a new directory is trickier - you'll need to add new includedirectories to the headers list in rebuild_include_HEADERS.sh, and new
source directories to the sources list in rebuild_libmesh_SOURCES.sh,
before you rerun each.