Control published files and folders in app classes folder in wtpwebapps

i am using eclipse helios 3.6.1 and WTP 3.2 with tomcat 7 and maven 2 as build tool, m2eclipse plugin.

when trying to run project on server from eclipse, i get endless exceptions this is opposite to running my project from maven tomcat plugin, everything works very fine

so i compared between the extracted war in target folder generated in my project (workspace/project/target/warFolder)

and the extracted war in (wtpwebapps/myapp)

and here are the contents:

1- (workspace/project/target/warFolder) contents:

com
messages
MET-INF
import.sql
log4j.properties

2- (wtpwebapps/myapp)

com
messages
MET-INF
import.sql
log4j.properties
src
target
.classpath
.project
file.txt
pom.xml

why it generates those additional unneeded folders? when i remove those additional folders and try to run project on server from eclipse it runs fine

so question is how to control eclipse or the m2eclipse or maven or whatever is causing the problem not to generate those folders, and why i get them in first place.

UPDATE: POM file plugins

<plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <configuration>
                    <source>1.6</source>
                    <target>1.6</target>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-dependency-plugin</artifactId>
                <executions>
                    <execution>
                        <id>install</id>
                        <phase>install</phase>
                        <goals>
                            <goal>sources</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>

            <plugin>
               <groupId>org.apache.maven.plugins</groupId>
               <artifactId>maven-resources-plugin</artifactId>
               <version>2.5</version>
               <configuration>
               <encoding>UTF-8</encoding>
               </configuration>
            </plugin>

            <plugin>

               <groupId>org.apache.tomcat.maven</groupId>
               <artifactId>tomcat7-maven-plugin</artifactId>
               <version>2.0-SNAPSHOT</version>
               <configuration>
               <path>/${project.build.finalName}</path>
               </configuration>


            </plugin>

        </plugins>

Solution

well i got this issue solved after removing the following entry from project deployment assembly:

Source: / Deploy Path: WEB-INF/classes

but any ideas why i had such entry in first place ?