A few changes have been made in the game files and directory-lookup logic to accomodate the modding community.
One notable change is the way buildings.xml references image resources. In previous versions, the buildings/building/graphics/@base attribute hosted a pattern to locate the image resource based on the tech/@id attribute value. This setting made the reusing of graphics for other races complicated: you had to copy the actual image to a different directory. In the new version, the image is directly references by the tech/@image attribute. See an example here.
The second notable change is the introduction of the dlc directory under the game's directory, where you can place your mods nicely and separated from other mods (previously, you had to dump everything into data).
You can have subdirectories denoting mods or zip files stored here. Each directory or zip file acts as a resource root similarly to the main zip files in the install directory, e.g., if you have a local resource generic/database/newrace.png, the file will be located under dlc/mymod/generic/database/newrace.png.
Note that the mod name doesn't provide a separate namespace, e.g., having multiple mods specifying the same local resource will overwrite each-other. This is especially true for skirmish/campaign like plugins: if you have a skirmish/human2/definition.xml, it might overshadow someone else's skirmish game. Therefore, I recommend using unique directory names below the language levels to avoid confusion:
See an example structure here.