Reformat index documentation

Move the paragraphs about running the reindex program and the index
names up to the top of the index section.  It makes more sense to
have them there, than in the middle of the setting descriptions.

Change-Id: I875a66173f752554803ca95bc166fba0dfbcd315
Add documentation of the index.threads setting

Change-Id: I4e7b737791968123d78c19ef558327609ef11b30
Escape dollar sign in plugin manifest entries

Escape dollar sign in plugin manifest entries, to prevent that
it is interpreted by the shell and thus get removed.

Change-Id: Iefd8abdcd207cb985f8156c7e41c094c1aa12b27