Made changes based upon freebsd/openbsd testing

Made changes based upon freebsd/openbsd testing

- Added better generally output formatting with warnings and blue info.
- Addressed deprecation warning when opening empty zip from temp file.
- Updated mysqldump so warnings did not stop dump, but are shown to
  users.
- Massively increased timeouts where needed.
- Fixed a few typos.
- Logged extra mysql known issues.
- Added protocol to mysql commands since that's what's expected in
  BookStack's usage.
- Updated required extensions list to be more comprehensive, based upon
  actual need on FreeBSD (Where php defaults were minimal) and extracted
  requirements to static class vars for easier editing.