Head Section

Your looking at a cutout of the head section of the basic index.php page of a Joomla Template.



Lines 3 thru 4 is a inside PHP tag with has comment area for the designer to add there Copyright & License information.

Lines 6 thru 7 is a security measure added to template for security reasons.

Line 9 is the Document Type for the template.

Line 10 HTML starter tag to the page also sets the Language type for the document this set by the Joomla back-end there is no need to edit code by hand
this is done via the back-end administration.
 
Line 11 the beginning of the HTML Head Tag.

Line 12 Jdoc include is parameter type is set head type.
This adds meta tag information which Joomla controls dynamically no need to add any meta tags or page title to the template page.

Line 13 is a CSS include tag with Joomla PHP code.
This points to the root templates folder were Joomla stores all front-end templates.
The "system" folder stores default templates for Joomla errors pages, offline pages and Styles etc.
It goes to the systems/css/system.css file which controls System Messages formatting.

Line 14  is a CSS include tag with Joomla PHP code. This points to the root templates folder were Joomla stores all front-end templates.
The "system" folder stores default template for Joomla errors pages, offline pages and Styles etc.It goes to the systems/css/general.css file  which controls system tooltips & editor button
formatting etc.

Line 15 is a CSS include tag with Joomla PHP code. This points to your current template CSS folder and the template.css this file is key in Joomla Template formatting.
By default Joomla uses only one CSS file. But the Joomla Template kit takes the template.css file breaks it into many files to make it easier to ID class to areas and debugging.

Line 16 thru 18 is a inside PHP a conditional tag which looks for right to Left languages like Arabic or Hebrew etc. If the condition is met then Joomla uses the "template_rtl.css" styles 
which is the last line of CSS code in included and overrides the standard left to right CSS styles.

The next section body tag and closing HTML tag.


This would make a basic Joomla 1.5.X Template index.php page.
There are other needed files but I'm sure that your starting to get it.