Use absolute paths so this works from any directory.
Abbreviate link to DiffPy-CMI main page.
Do not use HTML paths for internal links.

Internal links should be expanded with Sphinx HTML builder.
It is easier to check for link consistency and let them work
with other output formats.
Merge remote-tracking branch 'origin/source' into source.

Reverted change 39e1a17eb75fdec0be2e51a0bdc4fe0d98ee3765 to
abbreviations.txt.  PDFgetX3 paper has 2 co-first authors,
"and" is not a typo.
Reformat the Contents and Documentation paragraph.