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MPC uses the bundle data area to store mapping information between solutions and corresponding P2 bits. Unfortunately, that data is lost whenever MPC is updated or its OSGi bundle ID otherwise changes. I originally noticed this when working on bug 535039 and fixed it as part of that - assuming that this was a very minor change. Since this fix happened to cause bug 536385, I'm now documenting it here after the fact. The problem is caused by the OSGi data area being bound to the bundle id, which changes on update (and maybe other times). The fix is to use an org.eclipse.epp.mpc folder under the configuration area instead.
Unfortunately, the change caused bug 536385, as mentioned above. The cause was a conversion from the configuration area URL to URI. If the configuration area path contains a space, that space is not encoded in the URL and breaks the URI conversion. This was fixed in commit b1618565d6b17dc38751425def832f0936304828