Changing location of WebContent folder of Flash Builder/WTP Project
You can change the location of the default Web Application folder from <project>/WebContent to (i.e.) /src/main/webapp by making the following changes in Eclipse Project Properties.
Change the Web Deployment Assembly
Update build paths for:
- Flex SWCs Paths linked in Project Properties > Flex Build Path (Class libraries and Locale Bundles)
- Any compiler paths that might have referenced the old WebContent (ie services-config.xml)
Eclipse took care of the rest.