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Looks like the issue is releated with the error marker not being deleted. After editor reloading, the theory is loaded correctly (see tick in the Theories view), but the marker is not deleted.
A workaround is to delete the marker in Problems view for now. Need to check why the marker is not removed..
Theory imports are not loaded when typing on-the-fly and the error message remains even after restarting the editor.
To reproduce: create a new file Scratch.thy and start typing:
This results in an error: Bad theory file (file
"file:/home/necoro/isabelle/Isabelle2013/src/HOL/Library/RBT.thy")
The dependencies can be loaded after closing and re-opening the editor. However the error remains.
Investigate better loading on-the-fly as well as why the error is persistent.
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