You can build an eclipse project via a workspace from the command line:
eclipsec.exe -noSplash -data "D:\Source\MyProject\workspace" -application org.eclipse.jdt.apt.core.aptBuild
It uses the jdt apt plugin to build your workspace automatically. This is also known as a 'Headless Build'. Damn hard to figure out. If you're not using a win32 exe, you can try this:
java -cp startup.jar -noSplash -data "D:\Source\MyProject\workspace" -application org.eclipse.jdt.apt.core.aptBuild
Update
Several years ago eclipse replaced startup.jar with the "equinox launcher"
https://wiki.eclipse.org/Equinox_Launcher
On Eclipse Mars (MacOX):
java -jar /Applications/Eclipse.app/Contents/Eclipse/plugins/org.eclipse.equinox.launcher_1.3.100.v20150511-1540.jar -noSplash -data "workspace" -application org.eclipse.jdt.apt.core.aptBuild
The -data parameter specifies the location of your workspace.
The version number for the equinox launcher will depend on what version of eclipse you have.
Metadata should not be managed in source control. They contain mostly data relevant to your workspace.
The only exception is the .launch XML files (launcher definition).
They are found in
[eclipse-workspace]\.metadata\.plugins\org.eclipse.debug.core\.launches
And they should be copied into your project directory: When your project is refreshed, those configurations will be displayed in the "Run configuration" dialog.
That way, those launch parameter files can be also managed into the SCM.
(Warning: Do uncheck the option "Delete configurations when associated resource is deleted" in the Run/Launching/Launch Configuration preference panel: It is common to soft-delete a project in order to import it back again - to force a reinitialization of the eclipse metadata. But this option, if checked, will remove your detailed launch parameters!)
project-dir/.project
project-dir/.classpath
project-dir/.settings/*
should be in your SCM (especially .project and .classpath according to the Eclipse documentation).
The goal is that anyone can checkout/update his/her SCM workspace and import the Eclipse project into the Eclipse workspace.
For that, you want to use only relative paths in your .classpath, using linked resources.
Note: it is better if project-dir refers to an "external" project directory, not a directory created under the eclipse workspace. That way, the two notions (eclipse workspace vs. SCM workspace) are clearly separated.
As ipsquiggle mentions in the comment, and as I have alluded to in an old answer, you can actually save the launching configuration as shared file directly in your project directory. All launching configuration can then be versioned like the other project files.
(From the blog post Tip: Creating and Sharing Launch Configurations from KD)
Best Answer
Instead of using "Java Project from Existing Ant Buildfile", just create a simple "Java Project". In the wizard uncheck "use default location" and enter the path (or browse) to the top level directory of your existing project (i.e., where your build.xml is). True, eclipse will create .project and .classpath files in your project directory (if they do not already exist), but the project will remain outside the eclipse workspace.
Case in point, this setup has worked really well in a very particular situation on a standalone system where the source tree resides in a common location but each user has a workspace in a protected location. Using the method described above, each user of this system can create a project in their own eclipse workspace, execute ant targets and subsequently remove the project from their own workspace without affecting other users' workspaces.