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Generated Sources Root gone after every git pull in IntelliJ

One of the many modules I'm working on uses "generated-sources" for a couple auto-generated Java classes that the rest of the code depends on. Unfortunately, every single time I do a git pull it gets reset and I have to do mark the folder as "Generated Sources Root" again.
It's not a deal breaker, but it's really annoying. Isn't there a way to automate this? I don't know, some setting in IntelliJ or perhaps even directly in the pom.xml?

You can give a try to build-helper-maven-plugin and add more source directories to your project explicitly:
<project>
...
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>3.1.0</version>
<executions>
<execution>
<id>add-source</id>
<phase>generate-sources</phase>
<goals>
<goal>add-source</goal>
</goals>
<configuration>
<sources>
<source>${project.build.directory}/generated-sources/...</source>
</sources>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>
Also there is a little trick - actual source generation must happens before this goal execution.
In our project IDEA works pretty well with this approach.

Try adding generated-sources folder to git ignore file. Git ignore file if not already exists can be added in intelli idea like:
Then add generated-sources folder relative path like generated-sources/in git ignore file & commit .gitignore file. From next time any changes in that folder will not be overwritten or will be committed to server.

How to generate separate jar files for application, source, and documentation (for central.sonatype.org)

Sonatype has a repository that I want to deploy a jar file to, and they ask for separate files for application, sources, and javadocs:
Example:
example-application-1.4.7.pom
example-application-1.4.7.jar
example-application-1.4.7-sources.jar
example-application-1.4.7-javadoc.jar
In Scala SBT, I have a command called "package" that generates the jar file for the project, but that only generates "example-application-1.4.7.jar".
Question: What should I do to generate the other two jar files?

In Maven, in order to get the additional -sources and -javadoc artifacts, add to your POM file the following:
<build>
<plugins>
<!-- additional plugin configurations, if any.. -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>3.0.0</version>
<executions>
<execution>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.10.3</version>
<executions>
<execution>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
Note the snippet above:
We are invoking the Maven Source Plugin to create an additional jar files for sources
We are invoking the Maven Javadoc Plugin to create an additional jar files for javadoc
Executing
mvn clean package
You will find these two additional jars in the target folder.
The .pom file instead is generated during the install phase, but it is not placed under the target folder. Basically, it is a copy of your pom.xml file, with a different extension and used by Maven during the dependency mediation process to check which transitive dependencies are required by the concerned artifact.
Executing
mvn clean install
Maven will install the artifact in your local cache (in your machine), under path_to_cache/.m2/repository/your_groupId/your_artifactId/your_version/. In this folder, you will also find the .pom file, which normally you don't need to distribute (it is created automatically by Maven).
Further note: you probably don't want to generate these additional jar files at each and every build, so to speed up normal builds and have them only on demand, you could wrap the snippet above in a Maven profile.
You can achieve this by removing the snippet above from your build section and add a further section at the end of your pom:
<profiles>
<profile>
<id>prepare-distribution</id>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>3.0.0</version>
<executions>
<execution>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.10.3</version>
<executions>
<execution>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
</profiles>
So that normal builds would not create these jars anymore, but when executing the following:
mvn clean install -Pprepare-distribution
You would instead get them back. the -P option is actually activating on demand the profile defined with the id prepare-distribution.
With Maven 3 a default profile already comes as part of the super pom which perform exactly the same actions (sources and javadoc artifact), hence no need to add anything to your existing project. Simply run:
mvn clean install -Prelease-profile
Or, to activate it via a property
mvn clean install -DperformRelease=true
However, as also specified in the super pom, this profile may be removed in future releases (although there since first Maven 3 version till version 3.3.9 so far)
NOTE: The release profile will be removed from future versions of the super POM
The main reason behind this warning is most probably to push for the usage of the Maven Release Plugin, which indirectly makes use of this profile via the useReleaseProfile option of the release:perform goal.
As highlighted by comments, if you are not familiar with maven (especially via console) I would definitely recommend to
Go through the official Maven in 5 minutes documentation for a quick but worthy look.
Play with Maven from the command line, is there where Maven gives you its best. IDE integrations are great, but command line is the real turning point.
Then play with the POM customization above, to get familiar with some concepts and behaviors, first directly as part of your default build, then moved to a profile.
Then, and only then, move to the Maven Release Plugin usage. I recommend it as last step because you would already have acquired more confidence and understanding and see it as less magic and more reasonable approach.

How to start java app from Maven in non-base project folder?

I'm using Intellij Idea 14 and start learning embedded Maven installation.
At now Maven compile sources, generate JAR with MANIFEST.MF inside (with 'lib/' prefixes in 'Class-Path') to 'target/', copy dependencies at 'target/lib/' folder, copy folder 'src/main/resources/cfg' to 'target/cfg'.
If i manually go to folder 'target' and start app with 'java -jar app.jar' then it works fine and successfully find folder 'cfg', but if i start app from Idea then app triyng to search folder 'cfg' in base project folder.
There is some POM piece:
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
<version>1.4.0</version>
<executions>
<execution>
<goals>
<goal>exec</goal>
</goals>
</execution>
</executions>
<configuration>
<executable>java</executable>
<workingDirectory>${project.build.directory}\</workingDirectory>
<mainClass>app.Main</mainClass>
</configuration>
</plugin>
I looked at workingDirectory parameter [ http://www.mojohaus.org/exec-maven-plugin/exec-mojo.html ]. This won't work.
How can i change working folder to 'target'? This is for comfort app develop and run/debug right from Idea.
I need to get that result application structure:
/app.jar
/cfg
/cfg/application.cfg

Copying Maven Dependency into Project Structure

I've been stuck on one specific Maven task for a while now, and I haven't been able to find anything specific to it.
I'm trying to host a few files as a dependency in my internal Maven repository (Sonatype Nexus). The catch is, I need it to be placed into a specific folder in the project structure.
In other words, I need dependency A to be placed into /src/WebContent/VAADIN/themes/${project.name}/
Looking over this helpful page from the Maven website I was able to copy the dependency onto the hard disk in the exact location that I wanted, but it's not actually part of the project itself, so other classes have no idea it's there. Here's the exact code, though it's mostly a copy from the linked page:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.10</version>
<executions>
<execution>
<id>copy</id>
<phase>package</phase>
<goals>
<goal>copy</goal>
</goals>
<configuration>
<artifactItems>
<artifactItem>
<groupId>com.dsa.mobi</groupId>
<artifactId>DSAStyles</artifactId>
<version>1.0.0</version>
<type>jar</type>
<overWrite>true</overWrite>
<outputDirectory>${project.build.sourceDirectory}/main/webapp/VAADIN/themes/${project.name}/</outputDirectory>
</artifactItem>
</artifactItems>
</configuration>
</execution>
</executions>
</plugin>
Any help would be greatly appreciated, even if it's just a link to some documentation that might clear this up -- I looked over all of the XML documentation for Maven, which is confusing to find and more confusing to navigate, but I have yet to find a panacea for this >.>
Thanks in advance!
EDIT:
Here's an image of the folder structure in Eclipse's Project Explorer:
As you can see, only addons.scss and fisafetyapp.scss show up in this folder, whereas I'm trying to get Maven/the dependency to plug files into this exact location.
On disk, the dependency is being placed in this folder correctly, ie C:/myuser/fisafetyapp/src/main/webcontent/vaadin/themes/fisafetyapp/. However, it's not showing up in the Project Explorer, which keeps the other files from seeing it as the location is highly specific.

Your statement is right, not forget in your pom declaration to dependency:
<dependency>
<groupId>com.dsa.mobi</groupId>
<artifactId>DSAStyles</artifactId>
<version>1.0.0</version>
</dependency>

Copy the dependency with the maven-dependency-plugin into the src/main/resources folder in generate-resources phase (don't forget to add these files to source control ignore list). Then the resources plugin will automatically copy it into the target/classes folder and it will be also automatically added to your end artifact.

Proguard is saying it can't find any classes

I'm using proguard with a spring mvc application and maven.
My pom.xml's build section looks like:
<build>
<finalName>myapp</finalName>
<plugins>
<plugin>
<groupId>com.pyx4me</groupId>
<artifactId>proguard-maven-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>proguard</goal>
</goals>
</execution>
</executions>
<configuration>
<obfuscate>true</obfuscate>
<!--<options>-->
<!--<option>-keep public class</option>-->
<!--</options>-->
<injar>${project.build.finalName}</injar>
<injar>${project.build.finalName}</injar>
<inFilter>com.myapp.*</inFilter>
</configuration>
</plugin>
</plugins>
I also tried:
<injar>${project.build.finalName}.war</injar>
When I run:
mvn clean install
Build failure message:
[proguard] Reading program war [/Users/me/dev/git/myproject/myapp/target/myapp.war] (filtered)
[proguard] Error: The input doesn't contain any classes. Did you specify the proper '-injars' options?
ERROR] Failed to execute goal com.pyx4me:proguard-maven-plugin:2.0.4:proguard (default) on project myapp: Obfuscation failed (result=1) -> [Help 1]
It seems to have picked up my jar correctly as the messages before show:
[INFO] --- proguard-maven-plugin:2.0.4:proguard (default) # myapp ---
[INFO] execute ProGuard [-injars, '/Users/me/dev/gitserver/myproject/myapp/target/myapp.war'(!META-INF/maven/**,com.myapp.*), -outjars, '/Users/me/dev/git/myproject/myapp/target/myapp_pg.war', -libraryjars, ....
Also, what options do you suggest I use? This is a spring mvc so I have annotations like:
#Autowired
#Service
#Repository
#Controller
So any of those classes/fields should not be renamed I would imagine.
(My goal is just to make it a headache to someone who decompiles, such that they can't just decompile and use the code. Obfuscating will let them use it, but they won't be able to maintain the codebase unless they re-write it. I don't have any fancy algorithms so I have nothing really to hide in that respect.)
Update
Let me be clear here, my spring mvc using maven for some reason (I'm new to maven) when doing a mvn clean install produces both a myapp.war file and a exploded war myapp/ (this is what I want to deploy in production, not the myapp.war file)
My myapp folder has:
/target/myapp/
/target/myapp/meta-inf (empty folder)
/target/myapp/web-inf
/target/myapp/web-inf/classes (com.myapp. ...)
/target/myapp/web-inf/lib/
/target/myapp/web-inf/ web.xml, application.xml (for spring)
/target/myapp/web-inf/views/
So proguard should be obfuscating in the /target/myapp/web-inf/classes folder right?
How do I tell it to do so?
Update 2
I'm getting this now:
OK, I am not getting: failed to execute goal ...proguard .. Can't rename /Users/me/dev/git/project1/myapp/target/myapp/web-inf/classes (see my updates section for what I changed in my pom.xml)
I changed my pom.xml with:
<configuration>
<obfuscate>true</obfuscate>
<injar>${project.build.finalName}/WEB-INF/classes/</injar>
<inFilter>com/myapp/**</inFilter>
</configuration>

ProGuard filters work on file names, so
.....(!META-INF/maven/**,com.myapp.*)
probably won't match any class files. You probably want
.....(!META-INF/maven/**,com/myapp/**)
See ProGuard manual > Usage > File Filters

Can you post your entire pom?
Normally, Maven compiles to /target/classes (Even for WAR files) and the WAR plugin does the copy to web-inf/classes right before the package phase. You should not be manually compiling classes to web-inf/lib with Maven.
EDIT: OK this has take quite a bit of research, but I've found an answer for you. First, according to the ProGuard documentation, you should not have ANY classes in your war project:
Notably, class files that are in the WEB-INF/classes directory in a
war should be packaged in a jar and put in the WEB-INF/lib directory
You need to refactor your project so your web classes are built in a separate jar. Once you have built that jar project, you must add it as a dependency in your war project.
Once I created that setup, I was successfully able to build a war project with the following configuration:
<build>
<plugins>
<plugin>
<groupId>com.pyx4me</groupId>
<artifactId>proguard-maven-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>proguard</goal>
</goals>
</execution>
</executions>
<configuration>
<inFilter>com/example/**</inFilter>
<libs>
<lib>${java.home}/lib/rt.jar</lib>
<lib>${java.home}/lib/jsse.jar</lib>
</libs>
<options>
<option>-keep class com.example.echo.EchoServlet</option>
<option>-injar ${project.build.directory}/${project.build.finalName}.${project.packaging}</option>
<option>-outjar ${project.build.directory}/${project.build.finalName}-proguarded.${project.packaging}</option>
</options>
</configuration>
</plugin>
</plugins>
</build>
Note the "com.example.echo.EchoServlet". Since progaurd was going to change the name of my classes, I had to "keep" this servlet name so I could reference it in the WAR project's web.xml. If you use annotation based servlet configuration, I imagine this won't be necessary.