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Move "Project Sandboxing" to a separate section of the "Installation"
chapter since this is an advance topic which may confuse new users.
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- Fix minor formatting issues.
- Fix reference the gloassary TLS using ':term:'.
- Make sure nothing is between an anchor and the heading where ':ref:' references
the anchor. This meant moving all the recently added '.. index::' entries.
Update #3232.
Update #3229.
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- Change all suitable '.. include::' to TOC tree.
- Remove unused and not needed sections.
- Fix the conf.py to not exclude some files.
Close #3232.
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