Is the <version> a UIMA version, an Eclipse version, or a Maven version
number?

Thats a maven version number.

What does the <manifest>.ignore</manifest> mean?

Maven can generate a new manifest,  we do not want this cause
the version number in the pom.xml is not compatible with the version number which is required in a manifest file (must contain at least four number e.g. 2.2.0.0-xxx)

So in my opinion we should ignore the apache standard here and write 2.2.00 in the pom.xml
file as version for the plugins.

Can you post a link to something that describes how you figured out what
to put here?

There is some maven doc on the apache website.

http://maven.apache.org/plugins/maven-eclipse-plugin/eclipse-mojo.html

Hope this helps,
Jörn

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