Drupal theme registry alterations to allow theme functions, preprocess/process function to be organized like templates (.tpl.php).

template.php

<?php

/**
 * Theme templates, functions and preprocess/process functions
 *
 * Theme templates `*.tpl.php` files are stored in the `theme` directory along
 * with `*.func.php` and `*.vars.php` files. The latter two are enabled by the
 * processing done below. The three types of files can be grouped into
 * sub-directories. It is recommended that they are grouped by the modules
 * they originate from. Theme specific hooks should be grouped into a folder
 * named after the theme itself.
 *
 * Function files store theme functions directly related to the base file name
 * or "theme hook", e.g., the hook `foo` would be handled by the
 * `THEMENAME_foo` function which would be stored in `foo.func.php`.
 *
 * Variable files store preprocess and process functions directly related to
 * the base file name or "theme hook" just like function files, e.g., the hook
 * `html` would be handled by the `THEMENAME_preprocess_html` function held in
 * `html.vars.php`.
 *
 * The two types of files mentioned above should also be used to hold support
 * functions specific to the theming hook. When a function grows too large,
 * break it apart so it becomes more readable.
 *
 * Files specific to theme functions and variable preprocess/process functions
 * should be named after the `base hook`. Alternate hooks (or what is commonly
 * referred to as "hook suggestions") should not be used for the file name.
 * The contents of the theme functions file can hold hook suggestions and it
 * should be related to the base hook. Preprocess/process functions for hook
 * suggestions are not supported in Drupal core.
 *
 * Using these files will keep the `template.php` file clean and grouping them
 * within the theme directory will make it easier to discover and work with.
 * 
 * Warning: Using core's `path_to_theme` function may return the wrong path.
 * It was difficult to predict to begin with and the changes made here will
 * make it even worse. Use `drupal_get_path('theme', 'THEMENAME')` instead.
 */


/**
 * implements hook_theme().
 */
function THEMENAME_theme(&$existing, $type, $theme, $path) {
  // Custom theme hooks:
  // Do not define the `path` or `template`.
  $hook_theme = array(

  );

  // Process custom. This should be used again for any sub-themes.
  THEMENAME_hook_theme_complete($hook_theme, $theme, "$path/theme");
  // Process existing registry. This should be done only once from the base theme.
  THEMENAME_hook_theme_complete($existing, $theme, "$path/theme");

  return $hook_theme;
}

/**
 * Discovers and fills missing elements in the theme registry.
 *
 * Adds the following:
 *  - `includes` `*.vars.php` if variables file is found.
 *  - `includes` `*.func.php` if function file is found.
 *  - `function` if the function for $theme is found.
 *  - `path` if template file is found.
 *  - `template` if template file is found.
 */
function THEMENAME_hook_theme_complete(&$registry, $theme, $path) {
  $registry = drupal_array_merge_deep(
    $registry,
    THEMENAME_find_theme_includes($registry, '.vars.php', $path),
    THEMENAME_find_theme_includes($registry, '.func.php', $path),
    drupal_find_theme_functions($registry, array($theme)),
    drupal_find_theme_templates($registry, '.tpl.php', "$path")
  );
}

/**
 * Discovers and sets the path to each `THEME-HOOK.$extension` file.
 */
function THEMENAME_find_theme_includes($registry, $extension, $path) {
  $regex = '/' . str_replace('.', '\.', $extension) . '$/';
  $files = drupal_system_listing($regex, $path, 'name', 0);

  $hook_includes = array();
  foreach ($files as $name => $file) {
    // Chop off the remaining extension.
    if (($pos = strpos($name, '.')) !== FALSE) {
      $name = substr($name, 0, $pos);
    }
    // Transform - in filenames to _ to match theme hook naming scheme.
    $hook = strtr($name, '-', '_');
    // File to be included by core's theme function when the hook is invoked.
    // This only applies to base hooks. When hook derivatives are called
    // (those with a double '__'), it checkes for the base hook, calls its
    // variable processors and ignores anything specific to the derivative.
    // Due to the way it works, It becomes redundant to give it a path that is
    // not a base hook.
    if (isset($registry[$hook]) && !isset($registry[$hook]['base hook'])) {
      // Include the file so core can discover any containing functions.
      include_once DRUPAL_ROOT . '/' . $file->uri;
      $hook_includes[$hook]['includes'][] = $file->uri;
    }
  }

  return $hook_includes;
}