Fixes for submodule builds (WIP)

[joshmoore]

Trying to handle:

Traceback (most recent call last):
  File "/home/starfish/.conda/envs/scc/lib/python2.7/site-packages/scc/main.py", line 80, in entry_point
    (UpdateSubmodules.NAME, UpdateSubmodules),
  File "/home/starfish/.conda/envs/scc/lib/python2.7/site-packages/yaclifw/framework.py", line 188, in main
    ns.func(ns)
  File "/home/starfish/.conda/envs/scc/lib/python2.7/site-packages/scc/git.py", line 3161, in __call__
    self.merge(args, self.main_repo)
  File "/home/starfish/.conda/envs/scc/lib/python2.7/site-packages/scc/git.py", line 3192, in merge
    set_commit_status=args.set_commit_status)
  File "/home/starfish/.conda/envs/scc/lib/python2.7/site-packages/scc/git.py", line 1814, in rmerge
    allow_empty=allow_empty, is_submodule=True)
  File "/home/starfish/.conda/envs/scc/lib/python2.7/site-packages/scc/git.py", line 1820, in rmerge
    update_gitmodules=update_gitmodules, allow_empty=allow_empty)
  File "/home/starfish/.conda/envs/scc/lib/python2.7/site-packages/scc/git.py", line 1865, in summary_commit
    self.communicate("git", "commit", "-a", "-n", "-m", commit_message)
  File "/home/starfish/.conda/envs/scc/lib/python2.7/site-packages/scc/git.py", line 1101, in communicate
    raise Exception(msg)
Exception: Failed to run 'git commit -a -n -m merge master -Dall -Snone

Repository: spacetx/slicedimage
Already up-to-date.

'
    rc:     1
    stdout: HEAD detached at f4087ce
nothing to commit, working tree clean

    stderr:

[joshmoore]

0625c13 (now released as 0.10.0) was the ultimate fix. The rest of this consists of logging improvements and (slightly) saner chdir semantics. Both of which are probably worth having, but are not a must.