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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.

Spring boot additional Crash Command

According to the Spring boot documentation, it's possible to define additional command when using a remote shell based on Crash.
Default locations for these commands are classpath*:/commands/,classpath*:/crash/commands/
A property can be used to override the default locations but in the provided example, the custom command is located in resources.
In my opinion, custom commands (at least java commands) shouldn't be located in resources but in src/main/java.
It works fine when defining a custom path in resources but how can I define a custom path in src/main/java? Didn't find a way to do it for now!

If they're under src/main/java, they'll be compiled automatically which is not what you need. My solution was to simulate that directory as a resources folder, which in short translates to:
configure the compiler plugin to ignore that particular folder
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.3</version>
<configuration>
<source>${java.version}</source>
<target>${java.version}</target>
<excludes>
<exclude>crash/commands/*</exclude>
</excludes>
</configuration>
</plugin>
copy the files just like any regular resources in the target directory
<resource>
<directory>src/main/java/crash/commands</directory>
<targetPath>crash/commands</targetPath>
<filtering>false</filtering>
</resource>
Minor update & disclaimer:
As you may already know, there are a couple of closures which are executed on login/logout. At least with v1.3.1, which is what I'm blindly inheriting from spring-boot, it will pick the first login.groovy it finds in the classpath. My project's artifact is packaged in an RPM along with all the other dependencies. Since its name begins with r, it comes after crash.shell-1.3.1.jar which is where the defaults reside, so I had to do the following small hack to make it pick up my own scripts instead of the default ones:
<!-- hack to make CRaSH pick up login.groovy from our jar instead of the default one -->
<finalName>0_${project.artifactId}-${project.version}</finalName>

You can try to put your command at src/main/resources/commands/

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.

How to include external classes in my jar

I have a problem with a service I am trying to write. I am trying to create a service that runs in the background on a windows system but uses java. I have seen several ways of doing this, but decided on one method that seemed to meet my requirements. The service will check a database for items it needs to work on. When it finds an item in the DB that it needs to do it will run some system commands to take care of them.
I found a way to use the tomcat7.exe file to run a jar as a service and that worked pretty well for basic stuff. Anything I write and compile into my jar file "myService.jar" we'll can call it goes well enough. The problem is that we already have several classes written for accessing the DB and running commands that are precompiled in a library of classes called BGLib-1.0.jar.
I have used this library in writing several jenkins plugins and had no problems calling functions from it. They all work fine when I create an hpi file and deploy it in Jenkins. There the compiler (Eclipse using Maven) packages the BGLib jar in with the plugin jar and Jenkins figures out how to get them to see one another.
When I build my service jar, however, it doesn't work when I deploy it.
I run a command like this to install the Tomcat exe renames to myservice.exe:
d:\myService\bin>myService.exe //IS//myService --Install=D:\myService\bin\myService.exe --Description="run some commands
Java Service" --Jvm=auto --Classpath=D:\myService\jar\myService.jar;D:\myService\jar\BGLib-1.0.jar --StartMode=jvm --
StartClass=com.myCompany.myService.myService --StartMethod=windowsService --StartParams=start --StopMode=jvm --StopClass
=com.myCompany.myService.myService --StopMethod=windowsService --StopParams=stop --LogPath=D:\myService\logs --StdOutpu
t=auto --StdError=auto
When I deploy this with code solely within the myService.jar the service behaves as expected, but when I try to call functions within the BGLib-1.0.jar I get nothing. The jvm appears to crash or become unresponsive. Debugging is a little tricky but it looks like I am getting class not found errors.
I tried adding the entry below in the POM file to see if changing the classpath entry in the manifest would help, but it didn't change the manifest. I am still kind of clueless ass to how the manifest file works. Any documentation on that would be cool. I have been to Maven's site and it doesn't seem to have comprehensive documentation on the tags available. Is there something I need to change in the manifest to get my jar to see external classes? Or is there something I can add that will get Maven to compile the classes from that jar in with my jar?
thanks in advance.
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>com.myCompany.myService.myService</mainClass>
<customClasspathLayout>BGLib-1.0.jar</customClasspathLayout>
</manifest>
</archive>
</configuration>

To answer mainly the question of the title, you can the shade plugin to include dependencies into your final jar. You can even even relocate the class files (e.g. change package name) within the final jar so that the included classes don't conflict with different versions of the shaded dependency on the classpath. Not sure if this is the best solution for your particular problem though.

You can use the maven-dependency-plugin unpack-dependencies goal to include the contents of a dependency in the resulting artifact.
An example of how to do this would be:
<plugin>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<id>${project.artifactId}-fetch-deps</id>
<phase>generate-sources</phase>
<goals>
<goal>unpack-dependencies</goal>
</goals>
<configuration>
<outputDirectory>${project.build.outputDirectory}</outputDirectory>
<stripVersion>true</stripVersion>
<excludeTransitive>true</excludeTransitive>
<includeArtifactIds>protobuf-java</includeArtifactIds>
</configuration>
</execution>
</executions>
</plugin>
This will expand the protobuf-java dependency (flatten it) and include the contents in the resulting artifact generated by your build.

Looks to me you actually want to use the appassembler-maven-plugin, otherwise I'd go for the maven-shade-plugin.

Managing multiple Java modules with external resource dependencies

Suppose I have a set of n Java libraries each with a conf and a resources folder and then I have a Java project X that depends on some of these n Java libraries, how do I make it so that when X is built, all the dependent conf and resources folders are copied and merged in the dist folder. No - I don't want them to be embedded in the jars.
Obviously, there will be issues with duplicate filenames, but let's assume all files have distinct names.
Edit: An additional and related question: How do it so that project X can detect the conf and resources during development phase of all the dependent projects without needing to copy them over to project X's folder. For example, I'd like Netbeans to be able to find these resources that the referenced libraries use when I click "Run" on X's main method.
Edit2: Here's a hypothetical example of a project setup:
**Library 1:** Image Processing
conf: Processing configurations, log4j
resources: Training sets, etc.
**Library 2:** Machine Learning
conf: Training parameters, log4j
resources: Dependent C++ batch files (i.e. system calls)
**Library 3:** Reporting Tool
resources: Reporting templates
**Library 4:** Text Mining Toolkit
conf: Encoding, character sets, heuristics
resources: Helper PHP scripts
**Executable Project 1: **
Uses Library 1 to process images
Uses Library 2 to do machine learning on processed images
Uses Library 3 to make reports
**Executable Project 2: **
Uses Library 4 to do text mining
Uses Library 2 to do machine learning on collected textual information
Uses Library 3 to make reports
We can assume Executable Projects 1 and 2 can use different parameters for their constituent libraries once deployed.

Take a look at the maven-dependency-plugin which can copy the deps and copy them to particular location.
<project>
[...]
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.5.1</version>
<executions>
<execution>
<id>copy</id>
<phase>package</phase>
<goals>
<goal>copy</goal>
</goals>
<configuration>
<artifactItems>
<artifactItem>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>3.8.1</version>
<type>jar</type>
<overWrite>false</overWrite>
<outputDirectory>${project.build.directory}/alternateLocation</outputDirectory>
<destFileName>optional-new-name.jar</destFileName>
</artifactItem>
</artifactItems>
<outputDirectory>${project.build.directory}/wars</outputDirectory>
<overWriteReleases>false</overWriteReleases>
<overWriteSnapshots>true</overWriteSnapshots>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
[...]
</project>

I see the following in your example. Let me use Library 1 as an example.
Library 1: Image Processing
conf: Processing configurations, log4j
resources: Training sets, etc.
You have library 1 which contains processing configuration which sounds to me like a runtime configuration. This mean it should be part of the created jar (src/main/resources the location for such things). The same is for log4j configuration. Just put it into the jar (src/main/resources of the project.
Now comming to resources: Training set. If you make a separate maven project which contains a training set so this will produce a single artifact and can later be used to integrate that into the Example 1. If you have several training sets you can create different artifacts and use them as usual dependency or use the maven-dependency-plugin (or may be the maven-remote-resources-plugin) to use them in your projects.
With this setup you can deploy Library 1 into your local repository and of course into a repository manager and use it as a dependency.
You can use the same approach to handle Library 2, 3 etc.
May be you can take a look at the maven-remote-resource-plugin (I'm not sure if this helps).