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We're quite happily using wstool. It is deprecated in the favor of vcstool, but it works well. You can even have multiple .rosinstall files (e.g. per feature) and merge them via wstool merge to get a workspace with all dependencies.

There's also a non-written standard (used at least by our team and a lot of packages from ETH Zurich ASL) that each package can have a file dependencies.rosinstall in its root, and this specifies its from-source dependencies. We then have a script that recursively walks the workspace and merges all these files to the workspace's .rosinstall until all from-source dependencies are satisfied. But it is a bit fragile if e.g. two packages specify the same dependency but with different URL (e.g. one ending with .git and one without it).