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Declare resource included by maven-bundle-plugin as optional

I have a multi-module build creating multiple artifacts with package type "bundle".
Some of them create some information in the META-INF directory during compile time, some don't.
I tried to define an instruction in the parent pom.xml that adds the META-INF directory as a resource to the bundle.
Unfortunately this fails for those artifacts not creating the META-INF directory during the build time.
I tried to avoid defining this rule on all modules that currently DO creating the META-INF directory since
There is a lot and
maybe the others will create the META-INF directory in the future and this will require future developers to know that they have to add this directory as a resource now.
Is it somehow possible to make this "include-resource" instruction optional, meaning it ignores this resource if it's missing?
<plugin>
<groupId>org.apache.felix</groupId>
<artifactId>maven-bundle-plugin</artifactId>
<version>3.5.0</version>
<configuration>
<instructions>
<Include-Resource>META-INF=${project.build.outputDirectory}/META-INF</Include-Resource>
</instructions>
</configuration>
</plugin>

Prefixing the resource pattern with - should suffice, e.g.:
<Include-Resource>-META-INF=${project.build.outputDirectory}/META-INF</Include-Resource>
Documentation here.

How to get name of Maven dependency JAR (not full path) as a pom.xml variable

It looks like it is possible to get the path/to/a/dependency.jar as an expandable variable within a Maven pom.xml: see Can I use the path to a Maven dependency as a property? You can expand, e.g., an expression into a string like /home/pascal/.m2/repository/junit/junit/3.8.1/junit-3.8.1.jar.
What I want instead of the full path to the dependency JAR within my local Maven repository is just the bare name of the JAR, for example junit-3.8.1.jar.
So for example, within my pom.xml, I would like to be able to use a value like ${maven.dependency.junit.junit.jar.name} to expand to junit-3.8.1.jar.
Can I do this, and how?

You can use the maven-antrun-plugin to get the file name of a dependency. Ant has a <basename> task which extracts the file name from a path. As described in Can I use the path to a Maven dependency as a property? the full path name of a dependency is available in ant as ${maven.dependency.groupid.artifactid.type.path}. This enables us to extract the file name with the ant task like this:
<basename file="${maven.dependency.groupid.artifactid.type.path}" property="dependencyFileName" />
This stores the file name in a property named dependencyFileName.
In order to make this property availbable in the pom, the exportAntProperties configuration option of the maven-antrun-plugin needs to be enabled. This option is only available as of version 1.8 of the plugin.
This example shows the plugin configuration for retrieving the artifact file name of the junit dependency:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-antrun-plugin</artifactId>
<version>1.8</version>
<executions>
<execution>
<phase>initialize</phase>
<configuration>
<exportAntProperties>true</exportAntProperties>
<tasks>
<basename file="${maven.dependency.junit.junit.jar.path}"
property="junitArtifactFile"/>
</tasks>
</configuration>
<goals>
<goal>run</goal>
</goals>
</execution>
</executions>
</plugin>

No, I'm sorry to say that it isn't possible. So, you have two options before you.
1) modify the maven source code and contribute the modification.
2) write your own plug-in.
I recommend the second option. Writing plug-ins is not that hard. As a philosophical principal, select a frequently-used plug-in which has functionality close to what you want to accomplish. Read and understand the code, and then modify it to do what you desire.
So for your example, you might look at the filter plugin. There's also some interesting syntax going on in the Ant plugin. It allows you to name dependencies and get those jar filenames into the embedded Ant script.
Good luck. :-)
As a more practical alternative, you might just break down and manually code the property value with the exact version number you're using. You're not going to switch the version number that often, right? And this is only one jar you're dealing with, right?

Maven AppAssembler not finding class

Attempting to modify an existing Java/Tomcat app for deployment on Heroku following their tutorial and running into some issues with AppAssembler not finding the entry class. Running target/bin/webapp (or deploying to Heroku) results in Error: Could not find or load main class org.stopbadware.dsp.Main
Executing java -cp target/classes:target/dependency/* org.stopbadware.dsp.Main runs properly however. Here's the relevant portion of pom.xml:
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>appassembler-maven-plugin</artifactId>
<version>1.1.1</version>
<configuration>
<assembleDirectory>target</assembleDirectory>
<programs>
<program>
<mainClass>org.stopbadware.dsp.Main</mainClass>
<name>webapp</name>
</program>
</programs>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>assemble</goal>
</goals>
</execution>
</executions>
</plugin>
My guess is mvn package is causing AppAssembler to not use the correct classpath, any suggestions?

Your artifact's packaging must be set to jar, otherwise the main class is not found.
<pom>
...
<packaging>jar</packaging>
...
</pom>
The artifact itself is added at the end of the classpath, so nothing other than a JAR file will have any effect.

Try:
mvn clean package jar:jar appassembler:assemble

Was able to solve this by adding "$BASEDIR"/classes to the CLASSPATH line in the generated script. Since the script gets rewritten on each call of mvn package I wrote a short script that calls mvn package and then adds the needed classpath entry.
Obviously a bit of a hack but after a 8+ hours of attempting a more "proper" solution this will have to do for now. Will certainly entertain any more elegant ways of correcting the classpath suggested here.

I was going through that tutorial some time ago and had very similar issue. I came with a bit different approach which works for me very nicely.
First of all, as it was mentioned before, you need to keep your POM's type as jar (<packaging>jar</packaging>) - thanks to that, appassembler plugin will generate a JAR file from your classes and add it to the classpath. So thanks to that your error will go away.
Please note that this tutorial Tomcat is instantiated from application source directory. In many cases that is enough, but please note that using that approach, you will not be able to utilize Servlet #WebServlet annotations as /WEB-INF/classes in sources is empty and Tomcat will not be able to scan your servlet classes. So HelloServlet servlet from that tutorial will not work, unless you add some additional Tomcat initialization (resource configuration) as described here (BTW, you will find more SO questions talking about that resource configuration).
I did a bit different approach:
I run a org.apache.maven.plugins:maven-war-plugin plugin (exploded goal) during package and use that generated directory as my source directory of application. With that approach my web application directory will have /WEB-INF/classes "populated" with classes. That in turn will allow Tomcat to perform scanning job correctly (i.e. Servlet #WebServlet annotations will work).
I also had to change a source of my application in the launcher class:
public static void main(String[] args) throws Exception {
// Web application is generated in directory name as specified in build/finalName
// in maven pom.xml
String webappDirLocation = "target/embeddedTomcatSample/";
Tomcat tomcat = new Tomcat();
// ... remaining code does not change
Changes to POM which I added - included maven-war-plugin just before appassembler plugin:
...
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.5</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>exploded</goal>
</goals>
</execution>
</executions>
</plugin>
...
Please note that exploded goal is called.
I hope that small change will help you.
One more comment on that tutorial and maven build: note that the tutorial was written to show how simple is to build an application and run it in Heroku. However, that is not the best approach to maven build.
Maven recommendation is that you should adhere to producing one artifact per POM. In your case there are should two artifacts:
Tomcat launcher
Tomcat web application
Both should be build as separate POMs and referenced as modules from your parent POM. If you look at the complexity of that tutorial, it does not make much sense to split that into two modules. But if your applications gets more and more complex (and the launcher gets some additional configurations etc.) it will makes a lot of sense to make that "split". As a matter of fact, there are some "Tomcat launcher" libraries already created so alternatively you could use of one them.

You can set the CLASSPATH_PREFIX environment variable:
export CLASSPATH_PREFIX=target/classes
which will get prepended to the classpath of the generated script.

The first thing is that you are using an old version of appassembler-maven-plugin the current version is 1.3.
What i don't understand why are you defining the
<assembleDirectory>target</assembleDirectory>
folder. There exists a good default value for that. So usually you don't need it. Apart from that you don't need to define an explicit execution which bounds to the package phase, cause the appassembler-maven-plugin is by default bound to the package phase.
Furthermore you can use the useWildcardClassPath configuration option to make your classpath shorter.
<configuration>
<useWildcardClassPath>true</useWildcardClassPath>
<repositoryLayout>flat</repositoryLayout>
...
</configruation>
And that the calling of the generated script shows the error is depending on the thing that the location of the repository where all the dependencies are located in the folder is different than in the generated script defined.

Alternate Output Directory for JavaDoc

I'm trying to configure an alternate output location for the JavaDocs in my multi-module maven project. I configured the maven-javadoc in the parent POM to look like this:
<build>
...
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.9</version>
<configuration>
<noqualifier>all</noqualifier>
<reportOutputDirectory>
${project.reporting.outputDirectory}/api
</reportOutputDirectory>
<destDir>api</destDir>
</configuration>
</plugin>
...
</build>
And then here is where I set the project.reporting.outputDirectory.
<properties>
<project.reporting.outputDirectory>
./module-webapp/src/main/webapp/docs
</project.reporting.outputDirectory>
</properties>
However, Maven doesn't seem to care for the above configuration, and is outputting the JavaDoc in the default directory notwithstanding. Why is this?
Also, I used a relative path for my project.reporting.outputDirectory variable. Will this relative path mean the same thing when I run mvn javadoc:javadoc in the sub-modules as when I run it in the parent module?
Thanks in advance... much appreciated!

You need to change the name of your variable. project.reporting.outputDirectory is a built-in variable and maven is overriding your setting of it.
Note that you might still need to set the directory relative to project.reporting.outputDirectory, or something like ${basedir} to actually get this to work.
Also keep in mind, based on my reading of the documentation, your final directory will be ./module-webapp/src/main/webapp/docs/api/api, which may not be exactly what you want
as far as relative directories and submodules go, each build tends to be self-contained, so it will deposit javadocs relative to each sub build.

Found out what was wrong. For some reason, when I remove ${project.reporting.outputDirectory} and type in the path directly, it works. For some other reason, when I use any other variable name (other than the above) it works.

Environment Variable with Maven

I've ported a project from Eclipse to Maven and I need to set an environment variable to make my project work.
In Eclipse, I go to "Run -> Run configurations" and, under the tab "environment", I set "WSNSHELL_HOME" to the value "conf".
How can I do this with Maven?

You can just pass it on the command line, as
mvn -DmyVariable=someValue install
[Update] Note that the order of parameters is significant - you need to specify any options before the command(s).[/Update]
Within the POM file, you may refer to system variables (specified on the command line, or in the pom) as ${myVariable}, and environment variables as ${env.myVariable}. (Thanks to commenters for the correction.)
Update2
OK, so you want to pass your system variable to your tests. If - as I assume - you use the Surefire plugin for testing, the best is to specify the needed system variable(s) within the pom, in your plugins section, e.g.
<build>
<plugins>
...
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
...
<configuration>
...
<systemPropertyVariables>
<WSNSHELL_HOME>conf</WSNSHELL_HOME>
</systemPropertyVariables>
</configuration>
</plugin>
...
</plugins>
</build>

The -D properties will not be reliable propagated from the surefire-pluging to your test (I do not know why it works with eclipse). When using maven on the command line use the argLine property to wrap your property. This will pass them to your test
mvn -DargLine="-DWSNSHELL_HOME=conf" test
Use System.getProperty to read the value in your code. Have a look to this post about the difference of System.getenv and Sytem.getProperty.

You could wrap your maven command in a bash script:
#!/bin/bash
export YOUR_VAR=thevalue
mvn test
unset YOUR_VAR

For environment variable in Maven, you can set below.
http://maven.apache.org/surefire/maven-surefire-plugin/test-mojo.html#environmentVariables
http://maven.apache.org/surefire/maven-failsafe-plugin/integration-test-mojo.html#environmentVariables
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
...
<configuration>
<includes>
...
</includes>
<environmentVariables>
<WSNSHELL_HOME>conf</WSNSHELL_HOME>
</environmentVariables>
</configuration>
</plugin>

Following documentation from #Kevin's answer the below one worked for me for setting environment variable with maven sure-fire plugin
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<environmentVariables>
<WSNSHELL_HOME>conf</WSNSHELL_HOME>
</environmentVariables>
</configuration>
</plugin>

Another solution would be to set MAVEN_OPTS (or other environment variables) in ${user.home}/.mavenrc (or %HOME%\mavenrc_pre.bat on windows).
Since Maven 3.3.1 there are new possibilities to set mvn command line parameters, if this is what you actually want:
${maven.projectBasedir}/.mvn/maven.config
${maven.projectBasedir}/.mvn/jvm.config

There is a maven plugin called properties-maven-plugin this one provides a goal set-system-properties to set system variables. This is especially useful if you have a file containing all these properties. So you're able to read a property file and set them as system variable.

in your code add:
System.getProperty("WSNSHELL_HOME")
Modify or add value property from maven command:
mvn clean test -DargLine=-DWSNSHELL_HOME=yourvalue
If you want to run it in Eclipse, add VM arguments in your Debug/Run configurations
Go to Run -> Run configurations
Select Tab Arguments
Add in section VM Arguments
-DWSNSHELL_HOME=yourvalue
you don't need to modify the POM

You can pass some of the arguments through the _JAVA_OPTIONS variable.
For example, define a variable for maven proxy flags like this:
_JAVA_OPTIONS="-Dhttp.proxyHost=$http_proxy_host -Dhttp.proxyPort=$http_proxy_port -Dhttps.proxyHost=$https_proxy_host -Dhttps.proxyPort=$http_proxy_port"
And then use mvn clean install (it will automatically pick up _JAVA_OPTIONS).

I suggest using the amazing tool direnv. With it you can inject environment variables once you cd into the project. These steps worked for me:
.envrc file
source_up
dotenv
.env file
_JAVA_OPTIONS="-DYourEnvHere=123"

As someone might end up here changing his global Java options, I want to say defining _JAVA_OPTIONS is a bad idea. Instead define MAVEN_OPTS environment variable which will still be picked up automatically by Maven but it won't override everything like _JAVA_OPTS will do (e.g. IDE vm options).
MAVEN_OPTS="-DmyVariable=someValue"