Add argument to delete only PGDB redundant with input data.

[ArnaudBelcour]

When using the --clean argument with mpwt before a run on an input folder, all PGDBs are deleted.

With a new option (like --delete), only PGDBs redundant with the input files will be deleted.

Example:

Folder_input
├── species_1
│   └── species_1.gbk
├── species_2
│   └── species_2.gff
│   └── species_2.fasta
├── species_3
│   └── species_3.gbk

And species_1, species_2 and species_4 are in ptools-local.

Actually by using mpwt -f Folder_input --patho --dat --clean species_1, species_2 and species_4 are deleted inside ptools-local.

The new argument will only delete species_1 and species_2.

[ArnaudBelcour]

Modify --clean behaviour when using with -f input_folder. Now it will delete all PGDBs associated with the input folder.

[ArnaudBelcour]

Added in #27 .