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In my contrib/sampleapps/htmleditor I created a module addons where I wanted to keep all brandings. I have modified its layer to override files provided by component palette and favorites modules (explicitly to show their components by default). To my surprise, palette was visible and favories were not! This is very likely caused by ordering of modules on startup. As a rule (enforced by commit validation) if a module overrides a resource of another, it needs a dependency. So I tried to add dependency from UI - worked for component palette (as it has an API) but not for favorites - the build failed. I had to go to project.xml and keep just runtime deps there. Imho this can be hardly discovered by anyone except netbeans authors, so I would suggest the layer branding support to automatically add a runtime dep on modules which resources are overriden.
There is no branding support currently from the UI, but see issue #70884. That could add deps for you when branding existing layer items. You do not need to edit project.xml directly - you can just turn off the checkbox "use .... packages during compilation" in module dep GUI. *** This issue has been marked as a duplicate of 70884 ***
"There is no branding support currently from the UI" - there is, just create a module and edit its layer in context. I do not think that you can trade a defect for a feture, that is why I am reopening this bug: the support is there and in fact is broken, because without the runtime dependencies it creates a false impression that one can edit any layer and the changes will be visible.
Whatever you prefer, but it would only be solved as part of issue #70884.
Do not want to introduce artificial dependencies just for layer overrides. See issue #141925.
Would be feasible to solve using a weight attribute that would be added to any edited layer entry.