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Java: Proper organization of external libraries?

So I took a Coursera course that had me work with external libraries. Two .jar files which most of the weekly projects depended upon.
I'm not entirely sure how eclipse compiles and runs the files, and how it links to these external libraries -- what is the proper way of organizing this? Do I put a copy of each .jar file in each project directory?
Is there another, cleaner way that I should be organizing this?
Thanks --

As a beginner programmer it is OK to put it in each project. But consider that this is ongoing work and at some time in future you want to upgrade to a new version of these external libraries. Then you would have to copy it everywhere.
Instead another option is to store them in one place and add it in classpath in each project. Now you have only one copy of it, which is always better.
Now, if and when you do get a new version then the file names might change, so you will still have to change the classpath of each project.
But I advise you to worry about these and other such problems later. For now, focus on programming related problems rather than configuration.

If you want to maintain your libraries professionally in a formal manor then you're better of using a build tool like Gradle of Maven.
I'd suggest you to use Gradle to maintain the project since it has a whole lot of useful build tools available to you to use. Eclipse has a Gradle plugin available which allows you to use Gradle projects with it. See link below.
To give you a idea of how Gradle is used professionally. Android uses it by default to maintain their projects now. So Android java projects uses the Gradle build tool to maintain its library sources, compilation processes and such.
The difference between a Gradle project and a normal java project is that a Gradle project has a list of pre-defined scripts available to you which fetches the libraries, compiles them and prepares them before exporting the final bundle (jar). So really all Gradle does in before hand is fetch the libraries and prepares the specified tools before compilation so you won't need to mess with them your self. It prepares your project directory and remotely maintains your libraries so if they're available from a repository then it'll make sure to prepare them appropriately in before hand and setup your projects directories.
So really the difference you'd physically notice is that instead of using the default Eclipse export button to create your bundle (jar) you'd instead use a button from the side menu which the Gradle plugin adds and also you'd cleanly list the libraries in a structured order in a file that gets added to your project root.
If you want to get a basic understanding of how it works and really want to start to proffesionally or formally structure your project then try to create a very basic android app in Android Studio. see link below
If this isn't what you want at all and don't want to take it to this advanced level yet then adding the library bundles into some kind of lib folder that's located in your project root is properly best practice.
If you wonder why? Well basically different projects might use different versions of the library which may add or remove support to them. So to keep the versions consistent and make sure to have the right version available to you, you have the direct source near the project it self.
Here's some useful link:
http://www.vogella.com/tutorials/EclipseGradle/article.html
http://developer.android.com/sdk/index.html

Should I commit files that are changed by Eclipse?

I inherited a Java project in the form of an Eclipse project. After changing the Tomcat configuration (from v6 to v7), Subclipse prompted me to commit the following files:
.classpath
org.eclipse.core.prefs
org.eclipse.common.project.facet.core.refs
org.eclipse.common.project.facet.core.xml
Will commiting them help my team members or will it mess with their workspace?
What is the best practice approach to this?

Generally speaking, you should check-in (and commit after changes) everything that does contribute to the build AND is not re-generateable by re-building completely AND is workstation-specific. (The implications of this statement depend on your build process/procedure, which is intended.)
This implies you should exclude everything that is re-generated upon full build etc. so it is not checked in (and not offered for check-in).

As a general rule, you should avoid committing files that contain user preferences, and project details that that Eclipse and/or your plugins can regenerate.
But in some cases things are a bit murky. For instance, the .classpath file can be the primary source of the Eclipse build path; e.g. if you have JAR files in your project tree rather than using Maven. (With Maven, the m2eclipse plugin generates the .classpath file from the dependency information in the POM file, and hence the file should not be checked in.)
Also, some of the facet stuff is borderline. For instance, in projects with JSPs and Javascripts, I have found it essential to change the facet properties to disable broken validators. And there's a good case for treating those changes as part of the project rather than as personal preferences.
Separation of group / project preferences from personal preferences is one area where (IMO) Eclipse is seriously deficient.

It is better not to commit those files as paths/settings may differ on different workstations.
You may wanna use some build tool to overcome this. (eg. Maven)
As if any of the team members are not using eclipse (using some other ide) , those files have no meaning for them.
If everyone commits different IDE settings, imagine what kind of mess it can cause.
EDIT:
More explanation;
I have worked in teams that people used NetBeans, Eclipse, IDEA...for a really long time and it is not really an option for them to change the IDE. It will only affect the productivity of that person.
When people get used to their IDEs they learn shorcuts, they know where to look for some functions (refactor/generate getter setter/implement override required methods....) so if you force them to use some other IDE it will just make things harder for them and slower for the overall process. IMHO and from my experience having a flexible codebase is always good. I am an eclipse guy and probably would not want to work with any other IDE as I know lots of shorcuts which makes thing real quicker/easier for me and those shorcuts are different on different IDEs.
All IDE files can be regenerated automatical by the IDE itself probably in just a couple of clicks.
And my current project has 3 developers, each using different IDEs eclipse(me), NetBeans, IDEA without any problems. I dont want to see IDEA or NetBeans config files which makes no sense for eclipse when I check out the source from repo. Likewise for them as well.

Yes, though do make sure that paths are relative in the workspace rather than absolute paths. Having these files in the workspace allows members of your team to work in the same environment as you are. It also makes setting up a new development environment much easier: you just check it out of source control and in Eclipse use 'Import... > Existing Projects into Workspace'
As #adamdunne mentioned, these files can contain environment specific paths. However it if you are careful to make sure paths are relative within your workspace, by using variables and by not importing external jars, i.e., by only including jars from projects in the workspace, then you should be okay. In my workspace we check in those files and have had a lot less issues setting up dev. environments since.

I work in a project where we commit the .classpath file since it is very useful that all developers use the same :) If you only use dependencies inside your workspace, this file uses relative paths and thus should be same on all machines. Even if this file might not be necessary to build (with ant e.g.) it´s very convenient to synchronize it.
In contrast the org.eclipse.core.prefs stores (afaik) project-specific, but personal preferences of developers which I would not check in.
With the facets I didn´t work yet in a real project, so I can´t tell. But in general, I think it depends on the information in the file and on the way you work.
If you are unsure, just try it. If you get conflicts in these files all day this is a hint you may not be on the perfect way.

These files can be very useful to share configurations between developers. The alternative is to either use Maven (which is a huge task for an established project) or to have constantly-outdated step-by-step instructions and new developers taking half a day until they can even build the project.
However, you should take care to ensure that these configurations are portable, i.e. contain no local paths. This can be done via the use of relative paths within the workspace, eclipse path variables and user libraries.

What we've done is ignore these files, as they may mess up the workspace of others on the project.
Ignoring them also makes your project cleaner, which I always like.

These files can contain environment specific paths so I would suggest not checking them in. On my current project we use ant scripts to create the project and do the initial checkout of all our code.

Should I check-in IDE project files to version control system?

For a Java project (with the team of 5-10 developers) should I store my IDE project files (e.g. Eclipse or IntelliJ Idea) in version control system (currently I store only build scripts)? What's the best practice?
PS Do you aware of any tools to automatically generate project files for common Java IDEs according to some descriptor?

You might want to take a look at the answers to this question: Which eclipse files belong under Version Control. As to the second part, maven has plugins for IntelliJ and Eclipse at least.

If you care about the project file at all, then you should check it into a VCS. Really, you might not care. But if you do, VCS it...

Our team (6-8 developers) originally checked in project files, and soon found that they can cause problems when it comes to paths and build path, etc. Usually not, but when an issue did arise it could take time to ferret it out. Then we stopped doing that, and it has worked much better. We now put definitions in the VCS ignore files to make sure they don't get in. However, in our case we work with Maven, so the practice has been create an eclipse workspace and then import the Maven projects from the source. So recreating project environment is quick and predictable. From my experience, checking in can cause minor headaches.

There are different opinions. Once I was told that I shouldn't put project files in VCS, but then project files ware added to repository (not accidentally).
Many open source projects have project file in VCS. I think it could be good practice if one particular IDE is proffered in other case developers should probably take care on project files by themselves.
Maven can generate project files (at last for eclipse)

To check in, or not check in, the entire Eclipse project?

I'm soon going to check in the very first commit of a new Java project. I work with Eclipse Ganymede and a bunch of plug ins are making things a little bit easier.
Previously I've been part of projects where the entire Eclipse project was checked in. It's quite convenient to get the project settings after a check out. However this approach still was not problem free:
I strongly suspect that some Eclipse configuration files would change without user interaction (from when I used Eclipse Europa), making them appear as changed (as they were changed, but not interactively) when it's time to do a commit.
There are settings unique to each development machine as well as settings global for all developers on a project. Keeping these apart was hard.
Sometime if the Eclipse version was different from others Eclipse would get angry and mess up the project configuration. Another case is that it change the format so it gets updated, and if commited messes up the configuration for others.
For this specific project I have another reason not to commit the project files:
There might be developers who prefer NetBeans which will join the project later. However they won't join within the coming months.
How do you organize this? What do you check into versioning control and what do you keep outside? What do you consider best practice in this kind of situation?

At a minimum you should be check-in the .project and .classpath files. If anybody on your team is hard-coding an external JAR location in the .classpath you should put them up against the wall and shoot them. I use Maven to manage my dependencies but if you are not using maven you should create user libraries for your external JARs with with a consistent naming convention.
After that you need to consider things on a plug-in by plug-in basis. For example I work with Spring so I always check-in the .springBeans and likewise for CheckStyle I always check-in the .checkstyle project.
It gets a bit trickier when it comes to the configuration in the .settings folder but I generally check-in the following if I change the default settings for my project and want them shared with the rest of the team:
.settings/org.eclipse.jdt.ui.prefs - it contains the settings for the import ordering
.settings/org.eclipse.jdt.core.prefs - it contains the settings for the compiler version
In general I haven't noticed Ganymede modifying files without me modifying the project preferences.

I recommend to use maven so that the entire life cycle is outside of any IDE. You can easily create an eclipse project with it on the command line and you can use whatever you want, if it's not eclipse. It has it's quirks but takes out a lot of bitterness when it comes to dependencies and build management.

In our world, we check in the entire Eclipse project and the entire parallel but separate Netbeans project. Our motivations for this were entirely focused on "when I do a checkout, I want a functional configuration immediately afterward." This means that we had to do some work:
Create runnable configurations for each primary IDE (people like what they like). This includes main class, working directory, VM parameters, etc.
Create useful start up scripts for all of our relevant scenarios.
Create edited datasets that don't cause the checkout to take too much longer (it's a big project).
This philosophy was worth cash money (or at least labor hours which are almost more valuable) when our new hire was able to check out the project from Subversion into Eclipse and immediately run a functional system with a (small) real data set without any fuss or bother on his part.
Follow up: this philosophy of "make the new guy's life easier" paid off again when he changed IDEs (he decided to try Netbeans after using Eclipse for quite a long time and decided to stick with it for a while). No configuration was required at all, he just opened the Netbeans project in the same directory that Eclipse had been pointing to. Elapsed switchover time: approximately 60 seconds.

I only ever check in things are done by humans, anything else that is generated (whether automaticly or not) should be easy to regenerate again and is liable to change (as you've stated). The only exeption to this is when the generated files are hard (requires alot of human intervention ;) ) to get it right. How ever things like this should really be automated some how.

Try to port your project to a build system like maven. It has everything you need to get the same experience of the project on every machine you use.
There are plugins for just everything. Like the eclipse plugin. You just type "mvn eclipse:eclipse" and the plugin generates your entire ready to work eclipse project.
To give the answer to your question. Never check in files that are not being used by your project at any time in the development cycle. That means that metadata files like eclipse properties etc. should never be checked in in a SCM.

I like checking in the .project, .classpath, and similar files only if they will be identical on any Eclipse user's machine anyway. (People using other IDEs should be able to check out and build your project regardless, but that issue is orthogonal to whether or not to check in Eclipse-only files.)
If different users working on the project will want to make changes or tweaks to their .project or .classpath or other files, I recommend that you do not check them into source control. It will only cause headaches in the long run.

I use IntelliJ, which has XML project files. I don't check those in, because they change frequently and are easy to recreate if I need to.
I don't check in JAR files. I keep those in a separate repository, a la Maven 2.
I don't check in WARs or JARs or javadocs or anything else that can be generated.
I do check in SQL and scripts and Java source and XML config.

I'd suggest having the actual project files ignored by the version control system due to the downsides you mentioned.
If there is enough consistent information in the project settings that there would be benefit from having it accessible, copy it to a location that Eclipse doesn't treat as special, and you'll have it available to work with on checkout (and copy back to where Eclipse will pay attention to it). There is a decent chance that keeping the actual project files separate from the controlled ones will result in loss of synch, so I'd only suggest this if there is clear benefit from having the settings available (or you're confident that you'll be able to keep them synchronised)

In our case, we used to check in the project files (.project and .classpath) to make it easy for all developers to create their project workspace. A common preferences file and team project set were located in source control as well, so creating your workspace was as simple as import preferences and import team project set. This worked very well, but does rely on everyone having a consistent environment, any customizations would have to be applied after the basic workspace is created.
We still do this for the most part, but Maven is now used so of course dependency management is handled via Maven instead. To avoid conflicting information, the .project and .classpath were removed from source control and are now generated via maven goals before we import the team project set. This would easily allow for different environments, as you would simply need scripts to generate the IDE specific portions based on the Maven configuration.
PS-For ease of maintenance though, I prefer having everyone use the same environment. Anything else inevitably becomes a full time maintenance job for someone.

Netbeans 6.5 has an improved Eclipse project import which is supposed to sync changes from Netbeans back to Eclipse: http://wiki.netbeans.org/NewAndNoteWorthyNB65#section-NewAndNoteWorthyNB65-EclipseProjectImportAndSynchronization

Don't. Only check in the source code of your projects.

As a response to:
"There are settings unique to each development machine as well as settings global for all developers on a project. Keeping these apart was hard."
Eclipse offers a number of ways to keep local settings manageable: Java Classpath Variables (Java > Build Path > Classpath Variables) are one, 'Linked Resources' (General > Workspace > Linked Resources) are another http://help.eclipse.org/stable/index.jsp?topic=/org.eclipse.platform.doc.user/concepts/concepts-13.htm Creating a README that states which settings to set before building/running the project works pretty well in my opinion.
Now how to make sure your continuous build system understands the changes that were made to the eclipse settings, thats another issue... (I have a separate build.xml for ant that I keep up to date by hand)

Multi-IDE Support in Java for one Team

What is the best way to allow a team of programmers to use Netbeans, Eclipse and IntelliJ on the same project, thus eliminating the "which IDE is better" question.
Which files should or should not be checked into source code control?

I think the best way is to make the build process independent of IDE. This means that your project should not rely on any IDE-specific files to build, but rather use an external build system, like Apache Maven, Apache Ant, or even make or custom scripts. Maven is supported by most popular Java IDEs, either directly or via plug-ins.
If you don't want to use an external build systems, you should at least make the project as easy to set up as possible (i.e. by having standard folders for shared libraries and other dependencies). When I have working on teams with multiple IDEs in the past, I spent by far the most time on resolving dependencies as the prerequisites for building the project changed over time. In the worst case you may even end up with developers not bothering to get the latest version from the version control repository, since they think setting up the new project is such a hassle.
If your project has many library dependencies, I think its a good idea to make these available in binary form in the version control repository. That way people don't have to resolve all the dependencies of the dependencies and so on just to build a single project. This does however require that you have someone responsible for keeping the "official" binaries up-to-date whenever they change. (This is pretty much the same philosophy used by the Maven repository, but the principles can be applied manually even when not using Maven.)

Well, that's a pretty self-answering question.
The files to not check into source control are files that have to do with the IDEs themselves.
Leave it to the developers to generate these files.
If you use Maven, it can generate the files such as Eclipse's .project and .classpath for you. Eclipse in general is very easy to use with a basic file structure (with the new Java Project option).
I think Maven has Netbeans support as well, not sure about IntelliJ though.
Maven's site is maven.apache.org.

For each IDE that has more than one developer, check-in all the supporting files. Why re-invent the wheel at every desk.
I have done this with many different IDEs, and I have yet to see a filename conflict.
In fact, even when only a single developer uses a particular IDE, it is to his/her advantage to version the supporting files, for the same reason that you version the other files in your development environment: history, diffing, comments, etc.

For Eclipse, that would be .classpath and .project files.
My team uses Maven, and developers are discouraged from checking in Eclipse-specific files. Because they can be generated from Maven, these files are redundant.
Also, checking project-specific files seems like it would save time, but it usually winds up being a pain because of variations in different developers' workstations, resulting in wasted time resolving conflicts in the IDE-specific files. The only way to get around that is to force everyone to set up their environment the same way, which goes against the IDE-agnostic approach.

There are many considerations when using multiple toolsets within the same project team. For example, my team has Java developers using IntelliJ and most of the front end (JSP/CSS/HTML) developers using eclipse. We are in the process of migrating the Eclipse users to IntelliJ because of some IntelliJ plugins that we have developed that provide extended support for our environment. We're not going to develop the plugins for multiple platforms, so we are standardizing on IntelliJ across the board.
In terms of specific files, I can speak to IntelliJ. We have checked in our .ipr files and our .iml files. Do not check in .iws files. If you also have Eclipse users, configure your IntelliJ project to read/store dependency information in the .classpath file and commit that to your VCS.

We intentionally support multiple IDEs from the same SVN repository. Our thinking was that we want to ensure that, if a new person joined the team or someone had to start working on a new machine, we wanted them to be able to checkout the codebase, import it to the IDE and immediately have a work-able configuration.
What that means on the developer end is that they should not commit their changes to the IDE files. Everything else (e.g., src, test, lib and so forth) becomes the set that we normally update and commit every day.
The side benefit is that we have completely eliminated the IDE wars here: Netbeans and Eclipse people live in perfect harmony (looking askance at the IntelliJ people, but hey... ;-).

For more comments and answers on this topic see this question (How do you handle different Java IDEs and svn?)

We rename our IDE files for checkin with an extra extension .deletethis or similar. When a new person checks out the project, they simply strip off the extra extension and are good to go. This way we avoid source control conflicts with the project files as people tweak their environments. And you don't have to worry about educating new developers to not check in those files.

Typically, I would consider this a bad idea. I'm not sure what kind of environment this is (perhaps open source?), but it would really suck to support multiple IDEs. One thing I would recomend if this is unavoidable, would be to standardize your builds in ant scripts. If you have a large set of dependencies, this may be the easiest way to get a predictable build across all platforms.
If one of the IDEs happens to be RAD (based on eclipse), there is an entire folder called .settings that you would not want to include in the SCM.