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Not the generated MANIFEST.MF file in the folder src/main/webapp/META-INF of a maven based web application bundle is copied to the project's stage directory in virgo, but a default one that gets somehow generated by m2e. The content of the copied MANIFEST.MF in the stage directory is: Manifest-Version: 1.0 Build-Jdk: 1.7.0_10 Built-By: james Created-By: Maven Integration for Eclipse Please see https://bitbucket.org/ractive/virgo-tooling-problems for a sample setup.
The SpringSource tooling team is unlikely to be able to address this bug because of their current workload, so flagging as help wanted.
I am experiencing this issue under environment with Eclipse Juno (both on 3.8 and 4.2, actually STS 3.2.0.RELEASE), with Eclipse Virgo Tools 1.0.1, and with m2eclipse 1.3. This is a blocker and urgent!!! I can't even deploy any war application as though it is configured valid. Please, though being busy, reconsider dealing with this issue since this bug might be a crucial reason developers could decide to drop using Virgo.
(In reply to comment #2) You may wish to compare the Greenpages sample as that *was* working when it was refreshed a while ago. If it works with your combo of tooling, it would give you a starting point to compare with your application. Just a suggestion...