Failed project transformation from external jars to maven - eclipse

Question

I'm trying to transform my project from using external jars to maven. I've installed m2e plugin in Eclipse. However I can't configure it properly. I've generated a pom.xml file based on external jars, but there was one conflict jar - spring-orm-3.2.1.RELEASE.jar (it was twice on the list, maybe duplicated?). Then I erased jars from my /WEB-INF/lib directory and tried to deploy the project to Tomcat. When I choose in pom.xml Overview 'jar' as Packaging, I get:
2013-03-09 04:35:05 org.apache.catalina.loader.WebappClassLoader validateJarFile
INFO: validateJarFile(/home/apm/workspace/.metadata/.plugins/org.eclipse.wst.server.core/tmp0/wtpwebapps/keepGeo/WEB-INF/lib/tomcat-el-api-7.0.37.jar) - jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class: javax/el/Expression.class
2013-03-09 04:35:05 org.apache.catalina.loader.WebappClassLoader validateJarFile
INFO: validateJarFile(/home/apm/workspace/.metadata/.plugins/org.eclipse.wst.server.core/tmp0/wtpwebapps/keepGeo/WEB-INF/lib/tomcat-servlet-api-7.0.37.jar) - jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class: javax/servlet/Servlet.class
2013-03-09 04:35:05 org.apache.tomcat.util.digester.Digester endElement
SEVERE: End event threw exception
java.lang.NoSuchMethodException: org.apache.catalina.deploy.WebXml addServlet
2013-03-09 04:35:05 org.apache.catalina.startup.ContextConfig parseWebXml
SEVERE: Parse error in application web.xml file at file:/home/apm/workspace/.metadata/.plugins/org.eclipse.wst.server.core/tmp0/conf/web.xml
org.xml.sax.SAXParseException; systemId: file:/home/apm/workspace/.metadata/.plugins/org.eclipse.wst.server.core/tmp0/conf/web.xml; lineNumber: 103; columnNumber: 15; Error at (103, 15) : org.apache.catalina.deploy.WebXml addServlet
...
And when I choose other option 'war', 'pom', I get:
...
2013-03-09 04:47:14 org.apache.catalina.startup.ContextConfig processAnnotationsJar
SEVERE: Unable to process Jar entry [org/springframework/orm/ibatis/SqlMapClientTemplate$10.class] from Jar [jar:file:/home/apm/workspace/.metadata/.plugins/org.eclipse.wst.server.core/tmp0/wtpwebapps/keepGeo/WEB-INF/lib/spring-orm-3.2.1.RELEASE.jar!/] for annotations
java.util.zip.ZipException: invalid LOC header (bad signature)
I've tried to add <scope>provided</scope> to tomcat-el-api and tomcat-servlet-api dependecies in pom.xml, but with no success. I' ve also tried clean and build Maven/Project multiple times... Have no clue what to do next.
[edit]
pom.xml:
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>keepGeo</groupId>
<artifactId>keepGeo</artifactId>
<version>0.0.1-SNAPSHOT</version>
<repositories>
<repository>
<id>Geoserver-Manager</id>
<url>http://maven.geo-solutions.it/</url>
</repository>
</repositories>
<dependencies>
<dependency>
<groupId>org.eclipse.jdt.core.compiler</groupId>
<artifactId>ecj</artifactId>
<version>4.2.1</version>
</dependency>
<dependency>
<groupId>org.apache.tomcat</groupId>
<artifactId>tomcat-tribes</artifactId>
<version>7.0.37</version>
</dependency>
<dependency>
<groupId>org.apache.tomcat</groupId>
<artifactId>tomcat-jdbc</artifactId>
<version>7.0.37</version>
</dependency>
<dependency>
<groupId>org.apache.tomcat</groupId>
<artifactId>tomcat-jasper-el</artifactId>
<version>7.0.37</version>
</dependency>
<dependency>
<groupId>org.apache.tomcat</groupId>
<artifactId>tomcat-util</artifactId>
<version>7.0.37</version>
</dependency>
<dependency>
<groupId>org.apache.tomcat</groupId>
<artifactId>tomcat-jsp-api</artifactId>
<version>7.0.37</version>
</dependency>
<dependency>
<scope>provided</scope>
<groupId>org.apache.tomcat</groupId>
<artifactId>tomcat-el-api</artifactId>
<version>7.0.37</version>
</dependency>
<dependency>
<groupId>org.apache.tomcat</groupId>
<artifactId>tomcat-i18n-fr</artifactId>
<version>7.0.37</version>
</dependency>
<dependency>
<groupId>org.apache.tomcat</groupId>
<artifactId>tomcat-jasper</artifactId>
<version>7.0.37</version>
</dependency>
<dependency>
<groupId>org.apache.tomcat</groupId>
<artifactId>tomcat-i18n-ja</artifactId>
<version>7.0.37</version>
</dependency>
<dependency>
<groupId>org.apache.tomcat</groupId>
<artifactId>tomcat-catalina-ha</artifactId>
<version>7.0.37</version>
</dependency>
<dependency>
<groupId>org.apache.tomcat</groupId>
<artifactId>tomcat-api</artifactId>
<version>7.0.37</version>
</dependency>
<dependency>
<groupId>org.apache.tomcat</groupId>
<artifactId>tomcat-annotations-api</artifactId>
<version>7.0.37</version>
</dependency>
<dependency>
<groupId>org.apache.tomcat</groupId>
<artifactId>tomcat-catalina-ant</artifactId>
<version>7.0.37</version>
</dependency>
<dependency>
<scope>provided</scope>
<groupId>org.apache.tomcat</groupId>
<artifactId>tomcat-catalina</artifactId>
<version>7.0.37</version>
</dependency>
<dependency>
<groupId>org.apache.tomcat</groupId>
<artifactId>tomcat-dbcp</artifactId>
<version>7.0.37</version>
</dependency>
<dependency>
<groupId>org.apache.tomcat</groupId>
<artifactId>tomcat-i18n-es</artifactId>
<version>7.0.37</version>
</dependency>
<dependency>
<scope>provided</scope>
<groupId>org.apache.tomcat</groupId>
<artifactId>tomcat-servlet-api</artifactId>
<version>7.0.37</version>
</dependency>
<dependency>
<groupId>org.apache.tomcat</groupId>
<artifactId>tomcat-coyote</artifactId>
<version>7.0.37</version>
</dependency>
<dependency>
<groupId>antlr</groupId>
<artifactId>antlr</artifactId>
<version>2.7.7</version>
</dependency>
<dependency>
<groupId>org.antlr</groupId>
<artifactId>antlr-runtime</artifactId>
<version>3.5</version>
</dependency>
<dependency>
<groupId>commons-collections</groupId>
<artifactId>commons-collections</artifactId>
<version>3.2.1</version>
</dependency>
<dependency>
<groupId>commons-dbcp</groupId>
<artifactId>commons-dbcp</artifactId>
<version>1.4</version>
</dependency>
<dependency>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
<version>1.1.1</version>
</dependency>
<dependency>
<groupId>commons-pool</groupId>
<artifactId>commons-pool</artifactId>
<version>1.6</version>
</dependency>
<dependency>
<groupId>dom4j</groupId>
<artifactId>dom4j</artifactId>
<version>1.6.1</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>ejb3-persistence</artifactId>
<version>1.0.2.GA</version>
</dependency>
<dependency>
<groupId>org.hibernate.common</groupId>
<artifactId>hibernate-commons-annotations</artifactId>
<version>4.0.1.Final</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>4.1.10.Final</version>
</dependency>
<dependency>
<groupId>org.hibernate.javax.persistence</groupId>
<artifactId>hibernate-jpa-2.0-api</artifactId>
<version>1.0.1.Final</version>
</dependency>
<dependency>
<groupId>org.javassist</groupId>
<artifactId>javassist</artifactId>
<version>3.15.0-GA</version>
</dependency>
<dependency>
<groupId>org.jboss.logging</groupId>
<artifactId>jboss-logging</artifactId>
<version>3.1.0.GA</version>
</dependency>
<dependency>
<groupId>org.jboss.spec.javax.transaction</groupId>
<artifactId>jboss-transaction-api_1.1_spec</artifactId>
<version>1.0.0.Final</version>
</dependency>
<dependency>
<groupId>jstl</groupId>
<artifactId>jstl</artifactId>
<version>1.2</version>
</dependency>
<dependency>
<groupId>javax.transaction</groupId>
<artifactId>transaction-api</artifactId>
<version>1.1</version>
</dependency>
<dependency>
<groupId>org.jumpmind.symmetric.jdbc</groupId>
<artifactId>postgresql</artifactId>
<version>9.2-1002-jdbc4</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.7.2</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-simple</artifactId>
<version>1.7.2</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-aop</artifactId>
<version>3.2.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-beans</artifactId>
<version>3.2.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
<version>3.2.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context-support</artifactId>
<version>3.2.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-core</artifactId>
<version>3.2.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-expression</artifactId>
<version>3.2.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-jdbc</artifactId>
<version>3.2.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-config</artifactId>
<version>3.1.3.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-core</artifactId>
<version>3.1.3.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-taglibs</artifactId>
<version>3.1.3.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-web</artifactId>
<version>3.1.3.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-tx</artifactId>
<version>3.2.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
<version>3.2.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-webmvc</artifactId>
<version>3.2.1.RELEASE</version>
</dependency>
<dependency>
<groupId>taglibs</groupId>
<artifactId>standard</artifactId>
<version>1.1.2</version>
</dependency>
<dependency>
<groupId>it.geosolutions</groupId>
<artifactId>geoserver-manager</artifactId>
<version>1.3.0</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-orm</artifactId>
<version>3.2.1.RELEASE</version>
</dependency>
</dependencies>
<build>
<sourceDirectory>src</sourceDirectory>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.0</version>
<configuration>
<source>1.6</source>
<target>1.6</target>
</configuration>
</plugin>
</plugins>
</build>
<packaging>war</packaging>
</project>

Answer 1

You want to build a war.
For all the maven dependencies that are provided by your container (servlet jars etc...) you need to add the scope element.
For example
<dependency>
<groupId>org.apache.tomcat</groupId>
<artifactId>tomcat-api</artifactId>
<version>7.0.37</version>
<scope>provided</scope>
</dependency>
That way your classes will compile, but those jars will not get into the final build of your war.