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I want to build a project using two Git repositories. One of them contains of the source code, while the other has the build and deployment scripts.
My problem is that I need to have a repository for building and deployment of different parts of the project (big project, multiple repositories, same build and deployment scripts), but Jenkins does not seem to be able to handle this (or I don't know/didn't find how).
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Checking out more than one repo at a time in a single workspace is possible with Jenkins + Git Plugin (maybe only in more recent versions?). In section "Source-Code-Management", do not select "Git", but "Multiple SCMs" and add several git repositories.
Projects with multiple GitHub repositories All you have to do is select more than one GitHub repository when you create a new project. It's as simple as that. If instead, you want to add a repository to an already existing project, that's no problem either.
You can have as many remote repositories as you want, but you must give them different names.
UPDATE
Multiple SCMs Plugin is now deprecated so users should migrate to Pipeline plugin.
Old answer
Yes, Jenkins can handle this. Just use Multiple SCMs under Source Code Management, add your repositories and then go to the Advanced section of each repository. Here you need to set Local subdirectory for repo (optional) and Unique SCM name (optional).
Your repository will be pulled to the Local subdirectory which you have set so then you can build them in any order you want.
Updating per harishs answer - you need to install Multiple SCMs Plugin in order to achieve this functionality.
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