Checkpoint feature or tree and align modules does not work properly

[endixk]

If existing output directory is given, current version (v1.0.3) of the tree and align modules check the list of files that is already present in the directory to reduce running time by skipping some stages (which can be referred to as a checkpoint feature).

However it does not work properly if there happens to be an empty file with a proper name, or the file list is incomplete e.g. due to the interrupted process.

To produce a liable result, please only provide an empty/nonexistent output directory to these modules for now, until this issue being handled in the newer version.