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f5166695cb
* Break user guide into parts * Break up file I missed * Add basic .gitignore to suit out-of-tree builds in build, build1, build2 ... build9 * Small changes to autonumber.py for doc compilation This is a small change designed not to fix the incorrect logic of autonumber.py, but just to get the docs compiling. While assigning numbers, the code now just ignores the autonumber_by_chapter setting for a particular object if it can't find the appropriate section in section_numbers. This is a temporary fix! * Include part and chapter in autonumbered objects * Fix autonumber.py to correctly reference autonumber roles in file-level sections * Unify and simplify styling across documentation * Break dev docs down into individual chapter-files * Correct absolute links to relative * Disable browser suggestions for lunrsearch box in API docs * Remove part name from chapter 2.1 * Rename ambiguous 'Home' link to OpenMM.org * Typo * Minor fixes and reversions Reverts some changes I had made and later thought better of, and fixes some recurring typos across the documentation. * Number developers guide chapters * Fix responsiveness * Remove header.rst and center captions * Add a level of depth to main TOC and styling to accomodate * Add third level to Part-level TOCs * Use :numref: instead of :ref: to number links to sections * Continuously number chapters in user guide * navbar links to other docs relative, not absolute * Improve navbar spacing with new template * Fix sidebar while allowing it to scroll * Hard -> Soft links for navigation.html template * Add navigation.html template to cmakelists * Add another level of .. to relative links * Fix flex on C++ and remove layer of ..