Q:

Maven+Eclipse compilation fails, Maven compilation on terminal works

I am having a problem when trying to compile a Maven project from inside Eclipse Mars (4.5.1). 
Specs:

Win 7 SP1 x64
JDK x64 1.8.0_72
Eclipse x64 4.5.1
Maven 3.3.9

I believe this to be an Eclipse-Maven plugin interaction problem, as I am able to execute goals from the terminal such as:
mvn clean compile

mvn generate-sources

mvn install

In Eclipse, when I right-click on the project name and chose Maven install as the goal to execute, I get the following errors:

Scanning for projects
...
Building project-name-1.0-SNAPSHOT ...
[WARNING] The POM for com.sun.xml.ws:jaxws-rt:jar:2.2.10 is invalid,
  transitive dependencies (if any) will not be available, enable debug
  logging for more details
[INFO] --- jaxws-maven-plugin:2.3:wsimport (default) @ project-name
[WARNING] The POM for com.sun.xml.ws:jaxws-tools:jar:2.2.10 is
  invalid, transitive dependencies (if any) will not be available,
  enable debug logging for more details 
[INFO] Processing:
  file:/C:/project-name/src/main/resources/file.wsdl [INFO]
  jaxws:wsimport args: [-keep, -s,
  C:\project-name\target\generated-sources\wsimport, -d,
  C:\project-name\target\classes, -encoding, UTF-8, -Xnocompile,
  "file:/C:/project-name/src/main/resources/file.wsdl"]
[WARNING] Failed to build parent project for
  com.sun.xml.ws:bundles:pom:2.2.10
[WARNING] Failed to build parent project for
  com.sun.xml.ws:jaxws-tools:pom:2.2.10 
[WARNING] Invalid POM for
  com.sun.xml.ws:jaxws-tools:jar:2.2.10, transitive dependencies (if
  any) will not be available, enable debug logging for more details
[INFO] BUILD FAILURE
...
[ERROR] Failed to execute goal
  org.jvnet.jax-ws-commons:jaxws-maven-plugin:2.3:wsimport (default) on
  project project-name: Execution default of goal
  org.jvnet.jax-ws-commons:jaxws-maven-plugin:2.3:wsimport failed:
  String index out of range: -1 -> [Help 1]
[ERROR] To see the full stack trace of the errors, re-run Maven with
  the -e switch. [ERROR] Re-run Maven using the -X switch to enable full
  debug logging. [ERROR] [ERROR] For more information about the errors
  and possible solutions, please read the following articles: [ERROR]
  [Help 1]
  http://cwiki.apache.org/confluence/display/MAVEN/PluginExecutionException

However, if I execute mvn install from the terminal, the goal is successful!
I think I have all the necessary Maven plugins installed in Eclipse and the pom.xml file is correct, as via the terminal everything seems to work.
Hoping that someone will be able to hint into this problem.
EDIT: while mvn install fails in Eclipse, if I create a Maven Build configuration in Eclipse with goal mvn install -e, the problem does not happen. Passing this flag is somehow solving this problem.
EDIT: I paste the specific pom.xml section which triggers the problem in Eclipse (bold text is what Eclipse underlines in red):
<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>
    <!-- http://maven.apache.org/pom.html#Quick_Overview -->

    <groupId>group.name</groupId>
    <artifactId>project-name</artifactId>
    <version>1.0-SNAPSHOT</version>
    <packaging>jar</packaging>

    <name>${project.artifactId}</name>

    <properties>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
        <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>

        <maven.compiler.source>1.8</maven.compiler.source>
        <maven.compiler.target>1.8</maven.compiler.target>

        <wsdl.directory>${basedir}/../project-dep/src/main/resources</wsdl.directory>
        <wsdl.filename>file.wsdl</wsdl.filename>

        <mainclass>group.name.subname.TestApplication</mainclass>

        <ws.url>http://localhost:8081/sample-ws/endpoint</ws.url>

        <ws.name>Sample</ws.name>
        <uddi.url>http://localhost:9090</uddi.url>
    </properties>

    <dependencies>
        <!-- JAX-WS -->
        <dependency>
            <groupId>com.sun.xml.ws</groupId>
            <artifactId>jaxws-rt</artifactId>
            <version>2.2.10</version>
        </dependency>
        <!-- UDDI -->
        <dependency>
            <groupId>group.name.uddi</groupId>
            <artifactId>uddi-naming</artifactId>
            <version>1.0</version>
        </dependency>
        <!-- SOAP Handlers -->
        <dependency>
            <groupId>group.name.soap</groupId>
            <artifactId>ws-handlers</artifactId>
            <version>1.0</version>
        </dependency>
        <!-- JMockit - must appear before JUnit -->
        <dependency>
            <groupId>org.jmockit</groupId>
            <artifactId>jmockit</artifactId>
            <version>1.21</version>
            <scope>test</scope>
        </dependency>
        <!-- JUnit -->
        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
            <version>4.12</version>
            <scope>test</scope>
        </dependency>
    </dependencies>

    <build>
        <resources>
            <resource>
                <directory>src/main/resources</directory>
                <filtering>true</filtering>
            </resource>
        </resources>
        <testResources>
            <testResource>
                <directory>src/test/resources</directory>
                <filtering>true</filtering>
            </testResource>
        </testResources>
        <plugins>
            <plugin>
                <groupId>org.jvnet.jax-ws-commons</groupId>
                <artifactId>jaxws-maven-plugin</artifactId>
                <version>2.3</version>
                <executions>
                    <execution>
                        <goals>
                            <goal>wsimport</goal>
                        </goals>
                    </execution>
                </executions>
                <configuration>
                    <!-- https://jax-ws-commons.java.net/jaxws-maven-plugin/wsimport-mojo.html -->
                    <wsdlDirectory>${wsdl.directory}</wsdlDirectory>
                    <wsdlFiles>
                        <wsdlFile>${wsdl.filename}</wsdlFile>
                    </wsdlFiles>
                </configuration>
                <dependencies>
                    <dependency>
                        <groupId>com.sun.xml.ws</groupId>
                        <artifactId>jaxws-tools</artifactId>
                        <version>2.2.10</version>
                    </dependency>
                </dependencies>
            </plugin>
            <plugin>
                <artifactId>maven-failsafe-plugin</artifactId>
                <version>2.19.1</version>
                <executions>
                    <execution>
                        <goals>
                            <goal>integration-test</goal>
                            <goal>verify</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>org.codehaus.mojo</groupId>
                <artifactId>exec-maven-plugin</artifactId>
                <version>1.4.0</version>
                <executions>
                    <execution>
                        <goals>
                            <goal>java</goal>
                        </goals>
                    </execution>
                </executions>
                <configuration>
                    <!-- to prevent deprecation warning: -->
                    <killAfter>-1</killAfter>
                    <mainClass>${mainclass}</mainClass>
                    <arguments>
                        <argument>${ws.url}</argument>
                    </arguments>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.codehaus.mojo</groupId>
                <artifactId>appassembler-maven-plugin</artifactId>
                <version>1.10</version>
                <executions>
                    <execution>
                        <phase>install</phase>
                        <goals>
                            <goal>assemble</goal>
                        </goals>
                    </execution>
                </executions>
                <configuration>
                    <programs>
                        <program>
                            <mainClass>${mainclass}</mainClass>
                            <id>${project.artifactId}</id>
                        </program>
                    </programs>
                </configuration>
            </plugin>
        </plugins>
    </build>

</project>

This is my Maven installation inside Eclipse:

A:

First of all, if it works fine in the console, you have a project that be can importe in every IDE's who support Maven projects. It's a good news.
Secondly, check if the selected maven profile (repository configuration,...) is the same in console and in Eclipse.
Then you could check your configuration in the settings.xml (in your .m2 directory)
Maybe this previous answer could help too:
Maven ignores execution configuration

A:

Check in Maven > User Settings that User Settings points to the same archive than your Maven.
Did you try with the EMBBEDED one?

