Added base header and footer

This uses the HTML5 DOCTYPE
Integrated bootstrap files into theme

Added references to the extension points.

Added JQuery libraries from Google CDN which is needed by Bootstrap.
Added a Navbar with home and search capability
Added theme functions

The functions.php file will only be responsible for importing other PHP
files.

Each function library is stored in its own folder with the same name.

TODOs are added to the theme-options to indicate what options are going to
be provided to the theme user.
Added JQuery 1.9.1 libraries

Changed to use the local version to allow for offline development.
Added bootswatch CSS files

Only the CSS files are kept, the .gitignore was modified to ignore the
rest of the files that were included in the zip file:

https://github.com/thomaspark/bootswatch/archive/gh-pages.zip
Added Font Awesome 3.0

This will resolve problems on using icons from Bootstrap as they are not
scalable where Font Awesome icons are.

Only the css and font files are kept.
Theme customization and dynamic include

Theme specific functions and classes are put in the "trajano" namespace.

Error reporting made strict to reduce the chances of errors.

Theme customization implemented to support home icon, Bootswatch
selection, featured article backgroud image and sidebar location.

Droped the TODO of implementing a background image as the bootswatch will
take care of that.

All future PHP modules will be located in the include/ folder.
CSS files are enqueued from the css folder

This removes CSS declarations in the header and the style.css.
Home icon is now driven by theme customization
Javascript files are now enqueued from js

This allows new javascript files to be loaded up based on the contents of
the js folder.
Removed dynamic loading of Javascript files

This does not scan the folder as the JavaScript files need to be loaded in
a well defined order.
Dynamic switching of bootstrap theme on preview
Relocate site navigation bar to header file

This will allow index.php to focus more on the main area.
Made compatible with PHP 5.2

Removed PHP 5.3 constructs like namespaces and static member functions.
Added Masonry and specified JS dependencies
Post loop and UI generation to a new module

The index.php now loops through the posts.

UI generation functions to theme-ui.php.
Implemented dynamic sidebars with styling

Supports up to two levels of categories, recent posts, meta and tag cloud.

This does not support post counts, calendar or recent comments.
Added technologies used section

Updated infinite scroll to link to JetPack as that will be the technology
used to implement infinite scroll.
Added 404 page