Slightly expanded re-indexing intro
New CLI reindex commands
Clarify *when* to re-index
Migrate troubleshooting text to search.txt
Add note about fewer results during indexing
Fix indent in bullets
Clarify that FileAnnotations are not under 'annotation:'
Replace broken links with TODOs
Suggested improvements from Petr
More improvements of why corruption can occur
Handle double hyphen with mem
Use bold rather than italics
Fix 'Reasons that'->'Reasons why'
Merge pull request #890 from joshmoore/rebased/develop/new-search-docs

New search docs (rebased onto develop)