Add 'rescut' and 'bondoffset' keywords to 'prepareforleap'

[drroe]

Version 6.29.2.

Gives the user more flexibility by adding 2 new keywords to prepareforleap related to missing linkages search:

[rescut <residue cutoff>] Initial distance cutoff (default 8 Ang.) for residue center to residue center distance when looking for missing sugar linkages.

[bondoffset <offset>] Offset (default 0.2 Ang.) to add to “ideal” bond distances when looking for missing sugar linkages. Can be increased to accommodate distorted structures.

Also improve the missing linkage search under the hood by using residue center distances instead of residue first atom distances, which works better for somewhat distorted structures. Updates the manual.

I'm also adding a helper script in the doc subdirectory that should make it easier to update the PDFs of the manuals.