It is allowed to embed the Atlassian plugin framework in your own application. But what about additions to this framework, like Active Objects (and therefore also the Shared Access Layer)?
The Atlassian Plugin Framework is open source and essentially royalty-free for your use (note: I am not a lawyer). Check out the full licence details here: http://confluence.atlassian.com/display/PLUGINFRAMEWORK/License+and+Copyright+for+the+Atlassian+Plugin+Framework
Other supporting plugins like Active Objects will have their own licence terms that you'll need to chase up individually.
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