don't check template headers for header guard

it is almost impossible to get right and there is no reason for it to be right
add README.md
somewhat working, with examples and all, still need to do applications and the main pages
things are kind of working
things run through but indexes are broken
fix links to functions in cross ref
links to examples work
everything works except it is hard to get back to the main IMP project
things look pretty good
move doxygen handled files out of doc
everything works, perhaps, but lots of warnings to clean up
final cleanups
remove README.md