Added database port field to PHP and Java configure templates

cr https://cr.amazon.com/r/2264891/
Revert "Added database port field to PHP and Java configure templates"

This reverts commit fd8a3bf5dc8164c7c1bbea1c9b462f2ee37e4b04.
Revert "workaround to fix test for haproxy."

This reverts commit fde06dbaa5ce2ac8d509fadc2bc061558d0a51b6.
Make all cookbook tests pass.

Conflicts:
	mysql/specs/client_install_spec.rb
Fix autofs service and mount detection.

Needed for Amazon Linux:
- /etc/init.d/autofs does detect the service status correctly when used
  inside the restart function.
- The output format of mount changed which lets OHAI not detect all
  mounts. Related: https://tickets.opscode.com/browse/OHAI-453
Make bind mount check more resilient when there's no ephemeral device at all.

Use shellout instead of backticks and df to check mount point.

Use findmnt to have a portable way of checking bind mounts.
Remove logcheck/logtail, as it's actually not used - and logcheck installation fails on Amazon Linux 2014.03.
Do not use MySQL/Ganglia Layer dependet checks, as this is introduced only with Chef 11.10.

Avoid strictly start of gmond by overriding service start_command.
Configure a git user to prevent git from crashing while auto-detecting the email address.
Make Ganglia client service handling more robust.
Bump default passenger version to the latest bugfix release 4.0.41.

CR: https://cr.amazon.com/r/2336930/
Expose layers and hosts in opsworks.js.
Make the port for Node.js apps configurable and make it available to apps as PORT environment variable.
Add X-Request-Start header to nginx/unicorn Rails app configuration for NewRelic request queueing
Test whether RAID is considered as clean.
Changes to rails, PHP and Java to support RDS. Currently only rails
supports postgres

cr https://cr.amazon.com/r/2369582/
changed the php, rails and java cookbooks to use an attribute instead of
if/else in the template to handle the new port field in the database
config
changed default port on app/database info to be set by the deploy
cookbook, and fixed adapter field to reflect that it is now mapped in
the config JSON
added missing dependency on deploy cookbook to php and opsworks_java
cookbooks
added missing code to pass the java driver class to the webapp_context
template when the database is postgresql