Fix file_map being regenerated on every request.

A mistake a few months ago caused the file_map to always be regenerated
as Configure::write() would cause both Configure and Hash to be loaded,
invalidating the file map. By entering bootstrap mode earlier we can
avoid that.

Refs #5229
Merge pull request #5239 from cakephp/issue-5229

Fix file_map being regenerated on every request.