Alias Hierarchy

It appears you are working in the "master" branch in git. You should really be working in a version specific branch. The most direct documentation on this is Moving from a master branch to a version branch. For additional resources please see the documentation about release naming conventions and creating a branch in git.
Review of the master branch:

• Run coder to check your style, some issues were found (please check the Drupal coding standards):
  

  Severity minor, Drupal Commenting Standards, Internationalization, Drupal Security Checks, Drupal SQL Standards, Drupal Coding Standards
  
  sites/all/modules/pareview_temp/test_candidate/alias_hierarchy.module:
   +5: [minor] There should be no trailing spaces
   +25: [minor] There should be no trailing spaces
   +26: [minor] There should be no trailing spaces
   +95: [minor] There should be no trailing spaces
   +124: [minor] There should be no trailing spaces
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   +138: [minor] There should be no trailing spaces
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   +200: [minor] There should be no trailing spaces
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   +234: [minor] There should be no trailing spaces
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   +307: [minor] There should be no trailing spaces
   +316: [normal] String concatenation should be formatted with a space separating the operators (dot .) and the surrounding terms
   +317: [normal] String concatenation should be formatted with a space separating the operators (dot .) and the surrounding terms
   +320: [normal] String concatenation should be formatted with a space separating the operators (dot .) and the surrounding terms
   +336: [normal] String concatenation should be formatted with a space separating the operators (dot .) and the surrounding terms
   +385: [minor] There should be no trailing spaces
   +397: [minor] There should be no trailing spaces
   +424: [minor] There should be no trailing spaces
   +431: [minor] There should be no trailing spaces
  
  Status Messages:
   Coder found 1 projects, 1 files, 4 normal warnings, 23 minor warnings, 0 warnings were flagged to be ignored
  

• Remove "version" from the info file, it will be added by drupal.org packaging automatically.
• ./alias_hierarchy.module: The description on the line after the @param/@return documentation is either missing or not formatted correctly. See http://drupal.org/node/1354#functions
  

  256- * If the mlid is the lowest for the given link path.
  482- */
  

• Bad line endings were found, always use unix style terminators. See http://drupal.org/coding-standards#indenting
  

  ./alias_hierarchy.info:    ASCII text, with CRLF line terminators
  alias_hierarchy.info
  

This automated report was generated with PAReview.sh, your friendly project application review script. Go and review some other project applications, so we can get back to yours sooner.

See http://ventral.org/pareview/httpgitdrupalorgsandboxdjac1331114git

For the most part, things look pretty good.

My only concern would be with the possibility of XSS attacks ... the most likely culprit being inside of alias_hierarchy_form_alter:

// Display the path prefix (the part that goes before the custom alias).
$parent_menu_link = menu_link_load($node->menu['plid']);
$parent_alias = '';
if (!empty($parent_menu_link['link_path'])) {
  $parent_alias .= drupal_get_path_alias($parent_menu_link['link_path'], $node->language) . '/';
}
$form['path']['path_prefix'] = array(
  '#type' => 'textfield',
  '#title' => t('Path prefix'),
  '#default_value' => $parent_alias,
  '#description' => t("The prefix cannot be changed and is derived from the node's parents."),
  '#weight' => -1,
  '#disabled' => TRUE,
);

In this case, I'm not sure you can fully trust the drupal_get_path_alias() function to return 'safe' text; as the alias may be user-supplied, and Drupal's common pattern is to sanitize on output instead of input.

It felt like you may have been missing more check_plain() calls, but I'm assuming that pathauto_cleanstring() takes care of sanitization.

Other than that ... toss a sanitization function around $parent_alias (or explain why it isn't needed), and this is pretty much ready for an RTBC status.

Thanks for your patience, and sorry for the wait!

Okay ... being a textfield, the above should be okay.

Let's pass this on to the Git Admins. :)

Looks great.

Thanks for your contribution, djac! Welcome to the community of project contributors on drupal.org.

I've granted you the git vetted user role which will let you promote this to a full project and also create new projects as either sandbox or "full" projects depending on which you feel is best.

Thanks, also, for your patience with the review process. Anyone is welcome to participate in the review process. Please consider reviewing other projects that are pending review. I encourage you to learn more about that process and join the group of reviewers.

As you continue to work on your module, keep in mind: Commit messages - providing history and credit and Release naming conventions.