add option to keep extension

[hainm]

as we discused on gmail, I prefer to have an option to keep the extension.

.rst7.1 --> .1.rst7 .pdb.1 --> .1.pdb

Rationale: Many programs recognize files based on extension. So don't make it hard for user (to write his/her own renaming script).

PS: and .1.rst7 looks prettier (IMO).

updated

• [ ] keepext for clustering
• [ ] keepext for 'mask' command?

[drroe]

Hopefully addressed by #259

[drroe]

Done.

[hainm]

@drroe what do you think about adding 'keepext' for clustering too?

[hainm]

updated keepext for 'mask' command?