Ok I have build working now when I specify entries individually. Pasting my pom 
here for reference (giving only sample entries for includeClasses and 
includeFiles for reference as full project has lot of classes and assets):


<?xml version="1.0" encoding="UTF-8"?>

<!--


  Copyright 2008 Marvin Herman Froeder

  Licensed under the Apache License, Version 2.0 (the "License");

  you may not use this file except in compliance with the License.

  You may obtain a copy of the License at


  http://www.apache.org/licenses/LICENSE-2.0


  Unless required by applicable law or agreed to in writing, software

  distributed under the License is distributed on an "AS IS" BASIS,

  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

  See the License for the specific language governing permissions and

  limitations under the License.


-->

<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/maven-v4_0_0.xsd";>


<modelVersion>4.0.0</modelVersion>


<properties>

<flex.version>4.10.0.20130801</flex.version>

<flexmojos.version>6.0.1</flexmojos.version>

<flash.player.version>11.8</flash.player.version>

</properties>


<groupId>kiwikcore4</groupId>

<artifactId>kiwikcore4</artifactId>

<version>1.0-SNAPSHOT</version>

<packaging>swc</packaging>

<name>kiwikcore4 Library</name>


<build>

<sourceDirectory>src/main/flex</sourceDirectory>

<outputDirectory>target</outputDirectory>


<resources>

<resource>

<directory>src/main/resources</directory>

</resource>

</resources>


<plugins>

<plugin>

<groupId>net.flexmojos.oss</groupId>

<artifactId>flexmojos-maven-plugin</artifactId>

<version>${flexmojos.version}</version>

<extensions>true</extensions>


<dependencies>

<dependency>

<groupId>net.flexmojos.oss</groupId>

<artifactId>flexmojos-threadlocaltoolkit-wrapper</artifactId>

<version>${flexmojos.version}</version>

</dependency>


<dependency>

<groupId>com.adobe.flex</groupId>

<artifactId>compiler</artifactId>

<version>${flex.version}</version>

<type>pom</type>

</dependency>

</dependencies>


<configuration>

<includeFiles>

<include>fonts/Aller_Bd.ttf</include>


<include>images/contextMenu/defaultContextMenu.png</include>



<include>${project.build.sourceDirectory}/styles/ContextMenuStyle.css</include>


</includeFiles>


<includeClasses>

<include>com.guavus.library.components.breadCrumb.BreadCrumb</include>

<include>com.guavus.library.components.breadCrumb.events.BreadCrumbEvent</include>

</includeClasses>


<namespaces>

<namespace>

<uri>http://www.guavus.com/2013/kiwik</uri>

<manifest>kiwik-manifest.xml</manifest>

</namespace>

</namespaces>


<source-path>

<path-element>${project.build.sourceDirectory}</path-element>

<path-element>src/main/resources</path-element>

</source-path>


<fonts>

<managers>

<manager>flash.fonts.CFFFontManager</manager>

</managers>

</fonts>


<locales>

<locale>en_US</locale>

</locales>


<targetPlayer>${flash.player.version}</targetPlayer>


</configuration>

</plugin>

</plugins>

</build>


<dependencyManagement>

<dependencies>

<dependency>

<groupId>com.adobe.flex</groupId>

<artifactId>framework</artifactId>

<version>${flex.version}</version>

<type>pom</type>

<scope>import</scope>

</dependency>

</dependencies>

</dependencyManagement>


<dependencies>

<dependency>

<groupId>com.adobe.flex.framework</groupId>

<artifactId>flex-framework</artifactId>

<version>${flex.version}</version>

<type>pom</type>

<exclusions>

<exclusion>

<groupId>com.adobe.flex.framework</groupId>

<artifactId>playerglobal</artifactId>

</exclusion>

</exclusions>

</dependency>


<dependency>

<groupId>com.adobe.flexunit</groupId>

<artifactId>flexunit</artifactId>

<version>0.85</version>

<type>swc</type>

<scope>test</scope>

</dependency>


<dependency>

<groupId>com.adobe.flash.framework</groupId>

<artifactId>playerglobal</artifactId>

<version>${flash.player.version}</version>

<type>swc</type>

<scope>external</scope>

</dependency>


<dependency>

<groupId>com.adobe.flash.framework</groupId>

<artifactId>playerglobal</artifactId>

<classifier>en_US</classifier>

<version>${flash.player.version}</version>

<type>rb.swc</type>

</dependency>


<dependency>

<groupId>com.adobe.flex.framework</groupId>

<artifactId>textLayout</artifactId>

<version>${flex.version}</version>

<type>swc</type>

<scope>external</scope>

</dependency>


<dependency>

<groupId>com.adobe.flex.framework</groupId>

<artifactId>textLayout</artifactId>

<classifier>en_US</classifier>

<version>${flex.version}</version>

<type>rb.swc</type>

</dependency>


<dependency>

<groupId>com.adobe.flex.framework</groupId>

<artifactId>spark</artifactId>

<version>${flex.version}</version>

<type>swc</type>

<scope>external</scope>

</dependency>


<dependency>

<groupId>com.adobe.flex.framework</groupId>

<artifactId>spark</artifactId>

<classifier>en_US</classifier>

<version>${flex.version}</version>

<type>rb.swc</type>

</dependency>


<dependency>

<groupId>com.adobe.flex.framework</groupId>

<artifactId>sparkskins</artifactId>

<version>${flex.version}</version>

<type>swc</type>

<scope>external</scope>

</dependency>


<dependency>

<groupId>com.adobe.flex.framework</groupId>

<artifactId>rpc</artifactId>

<version>${flex.version}</version>

<type>swc</type>

<scope>external</scope>

</dependency>


<dependency>

<groupId>com.adobe.flex.framework</groupId>

<artifactId>rpc</artifactId>

<classifier>en_US</classifier>

<version>${flex.version}</version>

<type>rb.swc</type>

</dependency>

<dependency>

<groupId>com.adobe.flex.framework</groupId>

<artifactId>charts</artifactId>

<version>${flex.version}</version>

<type>swc</type>

<scope>external</scope>

</dependency>


<dependency>

<groupId>com.adobe.flex.framework</groupId>

<artifactId>charts</artifactId>

<classifier>en_US</classifier>

<version>${flex.version}</version>

<type>rb.swc</type>

</dependency>


<dependency>

<groupId>com.adobe.flex.framework</groupId>

<artifactId>spark_dmv</artifactId>

<version>${flex.version}</version>

<type>swc</type>

<scope>external</scope>

</dependency>


<dependency>

<groupId>com.adobe.flex.framework</groupId>

<artifactId>osmf</artifactId>

<version>${flex.version}</version>

<type>swc</type>

<scope>external</scope>

</dependency>


<dependency>

<groupId>com.adobe.flex.framework</groupId>

<artifactId>mx</artifactId>

<version>${flex.version}</version>

<type>swc</type>

<scope>external</scope>

</dependency>


<dependency>

<groupId>com.adobe.flex.framework</groupId>

<artifactId>mx</artifactId>

<classifier>en_US</classifier>

<version>${flex.version}</version>

<type>rb.swc</type>

</dependency>


<dependency>

<groupId>com.adobe.flex.framework</groupId>

<artifactId>advancedgrids</artifactId>

<version>${flex.version}</version>

<type>swc</type>

<scope>external</scope>

</dependency>


<dependency>

<groupId>com.adobe.flex.framework</groupId>

<artifactId>advancedgrids</artifactId>

<classifier>en_US</classifier>

<version>${flex.version}</version>

<type>rb.swc</type>

</dependency>


<dependency>

<groupId>com.adobe.flex.framework</groupId>

<artifactId>apache</artifactId>

<version>${flex.version}</version>

<type>swc</type>

<scope>merged</scope>

</dependency>


<dependency>

<groupId>com.adobe.flex.framework</groupId>

<artifactId>apache</artifactId>

<classifier>en_US</classifier>

<version>${flex.version}</version>

<type>rb.swc</type>

</dependency>


<dependency>

<groupId>com.adobe.flex.framework</groupId>

<artifactId>authoringsupport</artifactId>

<version>${flex.version}</version>

<type>swc</type>

<scope>merged</scope>

</dependency>


<dependency>

<groupId>com.adobe.flex.framework</groupId>

<artifactId>experimental</artifactId>

<version>${flex.version}</version>

<type>swc</type>

<scope>merged</scope>

</dependency>


<dependency>

<groupId>com.adobe.flex.framework</groupId>

<artifactId>experimental</artifactId>

<classifier>en_US</classifier>

<version>${flex.version}</version>

<type>rb.swc</type>

</dependency>


<dependency>

<groupId>com.adobe.flex.framework</groupId>

<artifactId>flash-integration</artifactId>

<version>${flex.version}</version>

<type>swc</type>

<scope>merged</scope>

</dependency>


<dependency>

<groupId>com.adobe.flex.framework</groupId>

<artifactId>flash-integration</artifactId>

<classifier>en_US</classifier>

<version>${flex.version}</version>

<type>rb.swc</type>

</dependency>


<dependency>

<groupId>com.adobe.flex.framework.automation</groupId>

<artifactId>automation_agent</artifactId>

<classifier>en_US</classifier>

<version>${flex.version}</version>

<type>rb.swc</type>

</dependency>


<dependency>

<groupId>com.adobe.flex.framework.automation</groupId>

<artifactId>automation</artifactId>

<classifier>en_US</classifier>

<version>${flex.version}</version>

<type>rb.swc</type>

</dependency>


<dependency>

<groupId>com.adobe.flex.framework.mobile</groupId>

<artifactId>mobilecomponents</artifactId>

<classifier>en_US</classifier>

<version>${flex.version}</version>

<type>rb.swc</type>

</dependency>


<dependency>

<groupId>com.adobe.flex.framework</groupId>

<artifactId>framework</artifactId>

<classifier>en_US</classifier>

<version>${flex.version}</version>

<type>rb.swc</type>

</dependency>


<dependency>

<groupId>com.adobe.flex.framework.themes</groupId>

<artifactId>halo</artifactId>

<type>swc</type>

<scope>theme</scope>

<version>${flex.version}</version>

</dependency>


<dependency>

<groupId>org.as3commons</groupId>

<artifactId>as3commons-reflect</artifactId>

<version>1.6.4</version>

<type>swc</type>

<scope>merged</scope>

</dependency>

</dependencies>


<profiles>

<profile>

<id>m2e</id>

<activation>

<property>

<name>m2e.version</name>

</property>

</activation>

<build>

<plugins>

<plugin>

<groupId>org.maven.ide.eclipse</groupId>

<artifactId>lifecycle-mapping</artifactId>

<version>0.9.9-SNAPSHOT</version>

<configuration>

<mappingId>customizable</mappingId>

<configurators>

<configurator id='org.maven.ide.eclipse.configuration.flex.configurator'/>

</configurators>

<mojoExecutions>

<mojoExecution>org.apache.maven.plugins:maven-resources-plugin::</mojoExecution>

</mojoExecutions>

</configuration>

</plugin>

</plugins>

<pluginManagement>

<plugins>

<plugin>

<groupId>org.apache.maven.plugins</groupId>

<artifactId>maven-resources-plugin</artifactId>

<version>2.4</version>

</plugin>

</plugins>

</pluginManagement>

</build>

</profile>

</profiles>


</project>


From: Poonam Anand <[email protected]<mailto:[email protected]>>
Date: Friday, 7 March 2014 6:58 PM
To: "Christofer Dutz [via Apache Flex Users]" 
<[email protected]<mailto:[email protected]>>
Cc: Jolly Paramjit <[email protected]<mailto:[email protected]>>
Subject: Re: AW: AW: AW: Flex mojos 6.0.1 and Flex SDK 4.10 - Facing problem 
with AS classes inclusion

Ok I missed this part - (this is actually quite important to add this before 
the Compiler). Changed order of dependencies and these errors are resolved. 
Still getting other errors, will let you know if need further help.

From: Poonam Anand <[email protected]<mailto:[email protected]>>
Date: Friday, 7 March 2014 6:48 PM
To: "Christofer Dutz [via Apache Flex Users]" 
<[email protected]<mailto:[email protected]>>
Cc: Jolly Paramjit <[email protected]<mailto:[email protected]>>
Subject: Re: AW: AW: AW: Flex mojos 6.0.1 and Flex SDK 4.10 - Facing problem 
with AS classes inclusion

Hi Chris,

I have already added dependency for this workaround but still the same error, 
have gone through all the documentation on confluence. Mentioned in below mail 
also, listing here again:

Also not I have added this dependency which is recommended fro resources
resolution:

            <groupId>net.flexmojos.oss</groupId>
            <artifactId>flexmojos-threadlocaltoolkit-wrapper</artifactId>
            <version>${flexmojos.version}</version>
          </dependency>

Poonam

From: "Christofer Dutz [via Apache Flex Users]" 
<[email protected]<mailto:[email protected]>>
Date: Friday, 7 March 2014 5:59 PM
To: Poonam Anand <[email protected]<mailto:[email protected]>>
Subject: AW: AW: AW: Flex mojos 6.0.1 and Flex SDK 4.10 - Facing problem with 
AS classes inclusion

I Think this is a known issue that has been observed since a while (probably 
more than 3 years) unfortunately I couln't quite find out where it's comming 
from but I documented a Workaround. 
https://dev.c-ware.de/confluence/display/PUBLIC/Configuring+your+poms
Have a look at the "things I recommend to Change" especially the additional 
plugin-dependency to flexmojos-threadlocaltoolkit-wrapper before the Compiler 
(this is actually quite important to add this before the Compiler).

Eventually this will help.

Chris

________________________________________
Von: Poonam Anand <[hidden email]</user/SendEmail.jtp?type=node&node=5337&i=0>>
Gesendet: Freitag, 7. März 2014 11:57
An: [hidden email]</user/SendEmail.jtp?type=node&node=5337&i=1>
Betreff: Re: AW: AW: Flex mojos 6.0.1 and Flex SDK 4.10 - Facing problem with 
AS classes inclusion

Yup thats correct :)

Ok so now I include all classes individually. Yes that is difficult task to
do (although replaced tags from .flexlibproperties) and anytime new
class/file added, we will need to update pom and pom file becomes
unnecessarily too big. I will log that bug.
But after this I started getting below error :

/Users/poonam.anand/kiwik_workspace/watermelon/kiwikcore4/src/main/flex/com/guavus/library/managers/AssetsManager.as(50):
col: 2: Error: unable to resolve '/images/dataGrid/buttons/max_normal.png'
for transcoding

        [Embed(source="/images/dataGrid/buttons/max_normal.png")]
 ^

/Users/poonam.anand/kiwik_workspace/watermelon/kiwikcore4/src/main/flex/com/guavus/library/managers/AssetsManager.as(50):
col: 2: Error: Unable to transcode /images/dataGrid/buttons/max_normal.png.

//AssetsManager class snippet

        [Embed(source="/images/dataGrid/buttons/max_normal.png")]
        [Bindable] public static var maxSkin:Class;

//pom

                                        <source-path>
                                                
<path-element>${project.build.sourceDirectory}</path-element>
                                                
<path-element>src/main/resources</path-element>
                                        </source-path>

src/main/resources has images folder. since I have given resources package
in source path and embedded image starts with /, it should be able to
resolve this by searching in specified source paths.

Also not I have added this dependency which is recommended fro resources
resolution:

            <groupId>net.flexmojos.oss</groupId>
            <artifactId>flexmojos-threadlocaltoolkit-wrapper</artifactId>
            <version>${flexmojos.version}</version>
          </dependency>




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