Developing with Eclipse Indigo (v3.7.2) requires Web Development Tools plugin v8.5.1(documentation).
For better integration you can use m2e-wtp plugin (documentation).
But WDT v8.5.1002.v20130402_2058 is not compatible with m2e-wtp v126.96.36.19930613-0136 (WDT dependencies rules exclude v1.0.0).
A workaround / hack exists (Stackoverflow thread), but it could be annoying later if you want update the plugin (the plugin signing change).
=> The best solution should be a WDT version v8.5.1003, with an update about m2e-wtp (as WDT v8.5.5). Could IBM team deploye this new artifact ? Thanks in advance.