Sorry you are running into this issue and the late response. On the line numbers, a few of projects around the MyEclipse core are thus protected due to licensing concerns; we are certainly one of the most pirated IDEs out there. I agree it would help in this case though, thanks for offering to help debug.
Is a WebTools dynamic web project which you have imported into MyEclipse? Or is this a regular Maven project that you have been working on outside the IDE. I have a few questions and suggestions:
1) Use the MyEclipse > Enhance WTP Project menu action on the project to see if it fixes the issue.
2) Send us your project at email@example.com
ATTN Brian with a link to this thread, that will allow me to examine your project directly and see what is going wrong/put a fix in.
3) Create a new MyEclipse Web project and enable Maven support. Copy your resources into this project, including the pom.xml, that will make this a MyEclipse web project which will not have issues reading deployment data.
I realize this is cumbersome but we have some defects around the *import* of Maven projects which we will be fixing in the MyEclipse 10 release.
I apologize for the inconvenience caused.