Update autogen scripts and templates for restructuring

The gen-formats-pages and gen-meta-support targets were also run, but
both resulted in no changes (since no new formats were introduced after
rc2).
Fix the formatting of the tutorial list
Fixes suggested by Roger
Formatting menu items correctly
Merge pull request #927 from melissalinkert/cli-docs

Add basic command line tool documentation
merge dev_5_0 -D org -I include -E exclude: PR 921 (Final BF doc updates for 5 release)
merge dev_5_0 -D org -I include -E exclude: PR 931 (Update autogen scripts and templates for restructuring)