Another two options are:

• Put a comment into the project description file. But since the comment might be replaced by anyone, so this would not be a good choice.
• Put the version as an argument of the Builder, this should work but feels really strange.

Did you try ProjectDescription.setVariableDescription(...) API, it supports adding more description to the .project file?

Here is an example:

<projectDescription>
...
	<variableList>
		<variable>
			<name>bspSchemaVersion</name>
			<value>0.1.0</value>
		</variable>
	</variableList>
</projectDescription>

Did you try ProjectDescription.setVariableDescription(...) API, it supports adding more description to the .project file?

Looks promising! I was not aware of this, thank you!