Menus cannot be themed differently

In addition to your proposal,

Wouldn't it be nice to do drupal_alter('menu_tree_output', $output, $menu_name) on the result of menu_tree_output()?

Rationale:

Overriding theme_menu_link() and theme_menu_tree() is nice, but inside these two functions you still don't know about the surrounding items. E.g., inside theme_menu_link() you don't know your position so you can't add 'odd' / 'even' classes.

Marked #408148: Create sub-theme functions for rendering menus as dup.

Looks great. We're a bit too late for #408150: Add "Welcome, $username" to user links but still nice to have

Please also see #653622: Make the '__' pattern for theme suggestions easier to use.

as per #9

I committed #653622: Make the '__' pattern for theme suggestions easier to use. This one will need a re-roll.

re-rolled.

In retrospect, it's probably a bit late for all three of these patches, but since I committed the first in the series, I guess we might as well finish the set. At least it doesn't break anything. :) (famous last words)

Committed to HEAD. Needs documenting in the theme upgrade guide.

I started to document this, but stopped, realizing that a bug that was fixed in D6, but not yet in D7 is preventing this particular use-case from working. I think it makes sense to have #241570: Theme preprocess functions do not get retained when using patterns get resolved before telling theme developers about this cool new toy that doesn't work yet.

Changing status to reflect #16.

#338027: Better menu template suggestion has been marked as duplicate

#241570: Theme preprocess functions do not get retained when using patterns landed, so: http://drupal.org/update/theme/6/7#theme-suggestions-for-menus.

Please see #588148-39: theme_links() is not really themeable for a still open question about how to best document the same for theme_links().

it doesn't work when the menu name is longer than one word.

[menu_name] => secondary-menu

you can't have dashes in php function names

themeName_menu_link__management -works

but it never pics up the secondary menu

intel_agate_menu_link__secondary_menu it's trying to match the - and not an underscore.

I would like to confirm #21.
As PHP does not allow dashes in function signatures using the proposed naming method does not work for newly created menus as new menunames are always prepended with menu.

No time to look into the theme suggestions so no further contributions there.