1) MyEclipse cleans out the classes folder when I do a rebuild, so it deletes struts.xml
You can go to Windows > Prefs > Java > Compiler > Building > Output Folder and uncheck “Scrub output folder while cleaning projects”. I guess that will fix this issue.
2) MyEclipse doesn’t show the classes folder in my project browser, so its a poor place to stick config files in the first place.
There is not way to show the classes folder in the package explorer. If you go to Windows > Show View > Other > Navigator then you should be able to see the WEB-INF/classes folder.
p.s. MyEclipse doesn’t support Struts 2 yet.