Make (most) HTML links to file formats work again

Make (most) HTML links to file formats work again

Now most generated program HTML pages again link to file formats where
the file format is mentioned in the help text.  With the current
replacement mechanism, it is tricky to get it to work exactly like it
used to before, so now all places that should become links are enclosed
in [REF]/[ref] pairs instead of silently turning any matching text into
a link.  This means that some text may no longer be converted into a
link where it should be, but on the other hand, log() in formulas is no
longer converted into a link to the log file format...

This patch only mechanically converted places where [TT].???[tt] was
mentioned into a link (there were no instances of [TT]???[tt]).  So any
place where a file format was mentioned without [TT]/[tt] is no longer a
link, but those can be fixed when noticed.

Change-Id: I119d6c0f69ed8c1ecfb12cf1f219a62148ab01e5