Fix links to Bio-Formats source code post-renaming

This commit should update the source code links to point at the new
formats-bsd, formats-gpl and formats-api folders of the Bio-Formats repository
Merge pull request #687 from jballanc/rebased/develop/11995b

Updated section on search re-indexing (see #11995) (rebased onto develop)
change TeX Gyre font package so XeLaTeX can find it
Merge pull request #688 from sbesson/formats_bf_renaming

Fix links to Bio-Formats source code post-renaming
Merge pull request #689 from mtbc/tex-gyre

change TeX Gyre font package so XeLaTeX can find it (rebased)
merge develop -D org: PR 626 (Add new Squash tutorial and screenshots)
merge develop -D org: PR 681 (Document Homebrew formula upgrade to 5.0.0 (rebased onto develop))