Doxygen: fixes for version >= 1.8.17

Description

• Given

    typedef struct tagABC { ... } ABC

  Doxygen 1.8.13 resolves link ::ABC but not ::tagABC, whereas Doxygen 1.8.17 resolved link ::tagABC but not ::ABC. Since these are incompatible, remove links entirely and replace with \c (except in SWIG interface files, where it's safer to use <tt>)
• Replace # with preferred :: for remaining links
• Fix Doxygen errors from nested comments; sometimes these are triggered by improper use of Doxygen commands, e.g using \dot{...} (which is a Doxygen command) for math, instead of putting in math mode i.e. \f$\dot{...}\f$
• Fix Doxygen errors from undocumented members

API Changes and Justification

Backwards Compatible Changes

• This change introduces no API changes
• This change adds new API calls

Backwards Incompatible Changes

• This change modifies an existing API
• This change removes an existing API

Review Status

N/A