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No programmatic solution yet, but there is a workaround: After upgrading Eclipse to 4.4, delete the file workbench.xmi in the Documents/.jcryptool/.metadata/.plugins/org.eclipse.e4.workbench directory once. This restores the toolbars, along with the missing "Operations," "Keystore," and "Algorithms" tabs permanently. (At least for me, with Eclipse Luna SR 1 on Windows 7.)
No toolbar available in Keystore view after Eclipse 4.4 migration
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