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Add project repo for an edited jar in Eclipse Maven project

I have a legacy project that I'd like to convert to a Maven project for dependency management.
The problem is, that I have one jar (fop-1.1.jar) that I had to edit. It differs from the one that is publicly available and I only have it locally. But I need it this way.
What I tried to do, following several similar how-to's, it to create a fake Maven repo inside the project (local repo is no good, because several people work on that project and the solution has to be self-contained on Git) and reference this repo from the pom.xml. Sounds like the way to go for me, but it doesn't work. Eclipse show the project repo grayed-out :(
What am I missing?
BTW: this is what I tried to follow: https://devcenter.heroku.com/articles/local-maven-dependencies

Let me suggest another way: When we need to "edit" a jar, we give it a special version number like 1.1-edited instead of 1.1.. Then we can easily upload it to our normal Maven repository and use it. Maven even makes sure that you do not accidentally load both versions in the same project because the edit is only in the version number.

I guess what you need is a private maven server(I guess it exists), and then execute command to deploy jar( before deploy, check your account has privileges)
mvn deploy:deploy-file -Dfile=${jarFilePath} -DgroupId=${groupID} -DartifactId=${artifactId} -Dversion=${version} -Durl=${privateServerURL} -Dpackaging=jar -DrepositoryId=${privateServerURLInYourMavenSettings.xml}
,
after deploy successfully, add maven dependency
<dependency>
<groupId>${groupID}</groupId>
<artifactId>${artifactId}</artifactId>
<version>${version}</version>
</dependency>

Maven deploy:deploy-file removes extension from file

I am trying to deploy signature files separately using deploy-file goal to Nexus staging repository, but I noticed that mvn deploy plugin removes the extension. My file is something like: azerty-0.1.jar.asc
but the file that gets deployed is: azerty-0.1.asc
I tried adding a classifier: -Dclassifier=jar
the file that gets deployed is: azerty-0.1-jar.asc
This seems like a strange behaviour.
Question: Any ideas how to work around it?

This is rather a normal behavior, Maven is using the file extension as artefact packaging, from maven-deploy-plugin, deploy-file, packaging option:
Type of the artifact to be deployed. Retrieved from the <packaging> element of the POM file if a POM file specified. Defaults to the file extension if it is not specified via command line or POM.
Note: bold is mine.
Moreover, the classifier option would indeed add an - between the version and the string provided as classifier: that's maven convention.
In your case you want to specify a special packaging, which would be jar.asc if you really want the remote file to have as extension jar.asc.
The following would hence work:
mvn deploy:deploy-file -Dfile=azerty-0.1.jar.asc -Dpackaging=jar.asc -DrepositoryId=your_id -Durl=http://your_repository -DgroupId=your_groupId -DartifactId=azerty -Dversion=0.1
Note the -Dpackaging=jar.asc which effectively tells Maven the file extension would be jar.asc.
As a general note, if you are using the repository as a build store, that would still be reasonable, otherwise in your case you would push to a Maven repository an artifact which would then be difficult (or rather weird) to import in a project.
If instead this is really an additional artifact of your project, you should look at the attach-artifact goal of the build-helper-maven-plugin, to effective define it as additional artifact, then Maven will automatically add it to its install and deploy phase.

Unknown small library (ex. webhdfs-java-client) in maven not found

I am trying to implement a little service in Scala using Maven to manage dependencies and I would like to add webhdfs-java-client that I have found at https://github.com/wdavidw/webhdfs-java-client
I have added to pom.xml following code:
<dependency>
<groupId>org.zxs</groupId>
<artifactId>webhdfs-java-client</artifactId>
<version>0.0.0</version>
</dependency>
It does not work, as I have expected. Does anyone could give me an advice if there exists some catalog of maven repositories (something like pip for Python)? And what can I possibly do if I'll not find this library in the catalog? Is it possible to somehow add it to maven manually?

In maven world you can install this dependency locally and resolution will be done via local cache (the one that usually resides in ~/.m2). Steps are as simple as mvn clean install in that repo. Having said this, it wouldn't resolve problem for your users (transitive dependencies, you know), which is why you likely need to publish that dependency somewhere (or ask library author whether it's published somewhere).
SBT, which is scala's de-facto build tool allows you to depend on other sbt flavored projects simply by referencing their git repository, but sadly, maven has no such feature.

Maven directory structure

I'm new to Maven and I've been reading all morning tutorials (amazing tool).
This new Java project I started looking at however doesn't use the default directory structure. Instead of src/main/java for sources it uses something like src/org/myapp.
When I run mvn package on the project (where pom.xml is located) I get a message saying that no Sources have been compiled because it's not able to find them (the source path being different).
Is there a way to specify your own sources path in Maven?

Add sourceDirectory to the build tag in the pom file.
<build>
...
<sourceDirectory>src</sourceDirectory>
...
</build>
Here is the relevant section in the maven docs.

In theory, you can use a non-standard directory structure for your Maven project. In practice, you may find that various Maven plugins and IDE integrations won't work properly. So I'd advise that you reorganize your project directory structure to be what Maven expects ... before you get lots of version control history and other stuff that will make reorganization more painful.

How did you create the project? The idea way to create a new maven project is: mvn archetype:create and then follow the instructions.
Read this for more details
Update to extend by answer based on the URL:
mvn archetype:create -DgroupId=[your project's group id] -DartifactId=[your project's artifact id]

Passing Maven Compiler Options From The Command-line

I am setting up several projects on a continuous integration server, some of which I don't have access to change the source code to, The server is a linux box, I am running into a problem where maven encoding needs to be changed to UTF8 to be able to compile on the box. Since I don't have access to modify the pom file, I was wondering if I can pass the compiler options as a command-line param? The project uses maven compiler 2.0 and I tried passing -Denconding=UTF8 without success.

You can use the Maven property "project.build.sourceEncoding".
So something along the lines of
mvn clean install -Dproject.build.sourceEncoding=UTF-8 should accomplish what you need.
This is equivalent of
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
in your pom.xml.
Edit: As a point of reference, there is the following link available POM Element for Source File Encoding showing the nuances between these properties for both Maven 2.0 and 3.0