Sorry for the late reply - I've been away on the West Coast.
There is no such thing as an indirect dependencies per OSGI. Either there are dependencies or there aren't. Please see the comments here that explain this in detail, review your manifests and let me know how it goes: [JBOSGI-794] WAB Fragment resources are not available through host - JBoss Issue Tracker
No worries. I still find it fast, if I get a reply to a forum post in under a week.
What I mean by indirect dependencies is that our WAR is dependent on OSGI bundle deployment.A, through "Dependencies: deployment.A" in MANIFEST.MF file of the .war. The indirect part comes from deployment.A having its set of dependencies through "Import-Package: org.B.package.path". Now our .war is indirectly dependent on "deployment.B".
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Have you tried using OSGI dependencies directly from your WAR files? You can do that: jbosgi/WebAppTestCase.java at master · jbosgi/jbosgi · GitHub
If you're dependent through Dependencies: it doesn't establish an OSGI dependency.
I have not tried this. I'm not at work tomorrow, but I will look into it on Monday and report back to you.
It seems weird that our WAR deployments manage to resolve all their dependencies, if they are deployed after Wildfly has already been started. If WARs are deployed during startup, they always fail to deploy after all OSGi bundles have been installed and before the first OSGi bundle is started.
I'll see if I can craft a test case. Could you file a bug for this in JBOSGI please?
I did not have time to test the fix you suggested yet. I did look through the bug report and couldn't find anything obvious that I forgot. If something is unclear, please ask and I'll add more details.