Working on fixing Cocoon issues.

Fixed repositories.
Configuration changes.
More clean-up.
Changed Saxon version.
Fixed CollateX version.
adding new files to this branch
Merged.
Fixed broken links and identifiers.
Yet another link-flipping demo.
Temporary to save from stash.
Parametrized algorithm is working (only via URL hack, but still).
Merge branch 'cocoon-cleanup' of github.com:umd-mith/mishnah into cocoon-cleanup
Merge branch 'flip' into cocoon-cleanup
Reran with Xerces 2.11, which doesn't rearrange processing instructions.
Merged.