The only things with non-obvious reasons are my removing of the brief descriptions of many of the Particle methods and the making of the internal state private. They are both to make the web page cleaner as it has many methods and the removed brief descriptions simply restated the functions name. Their effect was to make the methods list much longer and harder to read without providing any additional information.
Some of the changes touch other modules, either adding or fixing doxygen groups.
It also adds doc/internal to the doxygen search path as a place to put things like the introduction I have written (not submitted as it is still not stable). And it makes the list have paths on different lines as was discussed in a previous email.
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