yaniv_illouz,
I’m not very much familiar with the XML coding in javascript files. But, I suggest you to take a look at this thread which explains adding the xml code which is preceded with three slash marks (///) to the javascript file.
If that doesn’t help you, you can exclude the javascript file from validation at project level and also at workspace level. At project level, you can achieve it by right clicking on the project and select Properties > MyEclipse > Validation > Excluded resources, select the files you want to exclude from validation and click Apply and Ok.
If you want to disable the javascript validation at workspace level, you can do this by navigating to Window > Preferences > MyEclipse > Validation > uncheck both build and manual options for ‘Javascript validator for JS files’ > Click Apply and Click Ok.
Hope this helps and let us know if you see any issues.