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For example, you might have three repository directories, say, A, B, and C, where A is specific to one project, and B and C are common across many projects.
At this stage, Bamboo doesn't support having multiple checkout directories per build plan. However, you can work around this by setting these three directories up as separate Bamboo build plans, with B and C both being dependant on A (see 3.4 Triggering a Build when another Build finishes). This ensures that B and C will both build if you check-in source changes against A.
To make this work, you will also need to specify as an argument to your build scripts for B and C the location of A, which will be something like this:
../A/
Using a set up like this, your library module (A) should only be checked out once across the Bamboo instance.