Fix conary rdiff failing for misisng sub-troves and capsules (APPENG-3093)

If a sub-trove is removed in the newer version of a changeset, we need
to handle generating the diff differently. Essentially, we rely solely
on the infomration in the old trove. Also, if a capsule has changed,
then we can only say that the files differ, we cannot generate a diff.
Handle missing cap_sys_chroot=ep on python in test suite

When running the test suite, if the python executable being used
does not have cap_sys_chroot, skip the capsule tests that require
cap_sys_chroot and print a message documenting how to enable
those tests.
handle one remaining missing cap_sys_chroot=ep case
handle gid=0 != root (CNY-2867)

On AIX group 0 is 'system' instead of 'root'.
Fix file to directory rdiff (CNY-3863)
Clean up commit progress files after successful commit
Change use of malloc/realloc/free to PyMem_* versions

This fixes allocations on AIX and other platforms with different malloc
semantics.
Fix some bugs with the pure StreamSet implementation
Regenerate cython extensions
Suppress progress when downloading sources during a cook (CNY-3865)
Merge branch 'stable' into feldspar
2.5.4
Update makefile for 2.5.4