Document substitutions.
Update the sphinx integration docs.
Document project roots.
Revert the --git-dir behavior for 0.x.

This behavior will be off by default in the 0.x versions, and on by default in
1.x. 1.x should follow 0.x in history, so thus this commit.
Reinstate the --git-dir behavior for 1.x.

This reverts commit 62477d84df3d62547074abe3a77fc7370f9fa6d8.
Fix a test dependency.
Add some failing test cases.
Fix a test case; implement path translation.