htlatex command line to fix navigation links.

Most of the page header and footer navigation links (next, prev, tail,
etc.) inserted by htlatex in the multi-page version of the User Guide
were wrong. I found a comment on the web suggesting that this happens
to documents with footnotes unless the 'fn-in' option is used (which
puts foonotes on their parent page, I think). This did fix the problem.
Also follow through on renaming main file.

We recently renamed cug-html.html to cug.html, but some nav links
generated by htlatex, multi-page version, pointed to the original.
And avoid clash between the single- and multi-page CSS.

(see comments added to doc/Makefile)
Clearer comment in Makefile.
Use a custom exception for include-file not found errors.

This has no no effect except to raise an IncludeFileError instead of a
ConfigObjError, way was misleading (include-files are a cylc feature,
not from configobj).
Merge pull request #238 from hjoliver/html-multi-fix

Html multi fix
Merge pull request #239 from hjoliver/include-file-error-handling

Use a custom exception for include-file not found errors.