Fix a few bugs related to dumping files.

Fixes:

- Fix double print of header in dump_file.

- Fix a few possible file descriptor leaks.

- Add /d/ as another directory which should be skipped when printing out
  last mod time of a file.

- Fix possible crash if the path passed to _dump_file_from_fd is less than
  the length of one of the directory checks.

Change-Id: I450dfab76fd0ce4d4dca9ed39c82a980054f3cc3