Improve Diviner handling of paths and remarkup

Summary:

• Currently, the atomizers don't emit atoms with the right file in all cases. Make them always emit it correctly.
• Currently, we use absolute paths in some cases and relative paths in other cases. Use them consistently: relative when storing/presenting, absolute when accessing data.
• Don't preserve linebreaks when marking up documentation (documentation is generally wrapped at 80col, but should not be wrapped in this way when displayed).
• Markup Diviner link rules (albeit uselesly).

Test Plan:
Before:

{F33044}

After:

{F33045}

Reviewers: chad

Reviewed By: chad

CC: aran

Maniphest Tasks: T988

Differential Revision: https://secure.phabricator.com/D4992