Fixes from Blazej
Setting top_links via CLI
Adding plugins to settings via CLI
Merge pull request #536 from hflynn/11649

Adding JVM memory settings to main install docs
merge dev_4_4 -D org -I include -E exclude: PR 535 (Update homebrew git link (rebased onto dev_4_4))
merge dev_4_4 -D org -I include -E exclude: PR 537 (Web settings removal 11559)