fix php cart PEAR builds

1. php control script cleanup

2. fix php cart PEAR builds
>     - ignore checking for php extensions, as they're not PEARs
>     - do not fail on upgrading PEAR to the same specific version
>     - upgrade each PEAR with all dependencies
>     - prevent malforming PEAR cache&registry files
>     
>     Bug 1047473 - Fail to install missing dependencies to PHP-5.4 app via
>     deplist.txt - https://bugzilla.redhat.com/show_bug.cgi?id=1047473
>     
>     Bug 1045338 - Failed to create drupal quickstart with php-5.4 cartridge
>     in INT - https://bugzilla.redhat.com/show_bug.cgi?id=1045338
>     
>     Bug 1046048 - Mail PEAR causes errors during deploy, no email
>     capabilities - https://bugzilla.redhat.com/show_bug.cgi?id=1046048
>     
>     Bug 977036 - PHP gear creating throwing PEAR warnings to platform
>     logs - https://bugzilla.redhat.com/show_bug.cgi?id=977036

3.  fix php-cli include_path; config cleanup    
>     - Fix include_path when php is invoked from command line
>     - Remove double-slashes from Apache/PHP configuration files