implemented "includeFile()", minor coding standard whitespace
Remove search "this/all" options, site by default (if configured)
Updated defaults to be set before including site configuration, mainly to support $HEAD = true page configuration with additional site configuration.  Removed meta keywords and description variables, can be configured into $HEAD in site/page configuration.
Removed keywords and description from php variables documentation
Added includeFile documentation to phpFunctions.md
Corrected documentation of where $HEAD markup is inserted
Added links from navItem(), navGroup() to $NAVIGATION
removed reference to DOCUMENT_ROOT/site, /path/to.  Added most commonly used variables to examples.  Referenced flexible-grid content pattern.  described apache configuration
Updated embedding to show a plus (+) at the start of added lines
Corrected rewrite rule from /template to /theme
Added sections for "installing" and "using" the template
Fixed documentation of navItem
Added navigation example image, updated navigation variable description
Reorganized phpVariables page
Added jump links for most common variables, moved general layout to bottom, fixed headers
Added $CONTACT_URL variable
describe where to put theme css, updated comments for php example
Added link to content patterns, and flexible grid pattern
Moved test folder to example
Only output page-footer element if it has content