actually this is a java version related issue. since this project has is dependent to a java project running in a server with java 6 we have downgraded the project from java 7 to java 6.
i have changed runtime, build path and pom.xml pointing to java 6. but, forgot to change in web.xml header endpoints.
because of that , when updating the project, eclipse got struck up to find that this is a web project.
from (java 7)
<web-app xmlns:xsi="http://www.w3.org/2001/xmlschema-instance" xmlns="http://xmlns.jcp.org/xml/ns/javaee" xsi:schemalocation="http://xmlns.jcp.org/xml/ns/javaee http://xmlns.jcp.org/xml/ns/javaee/web-app_3_1.xsd" id="webapp_id" version="3.1">
to (java 6)
<web-app xmlns:xsi="http://www.w3.org/2001/xmlschema-instance" xmlns="http://java.sun.com/xml/ns/javaee" xsi:schemalocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/web-app_3_0.xsd" id="webapp_id" version="3.0">
after this change, on "maven-> update project" i got the proper project setup.
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