I have a custom script. It selects all the source files, strips any license headers and concatenates them like this:

    <source_file name="foo/bar/Baz.java">
    ...
    </source_file>

It then chunks them to fit within model context window limits, sends it to the LLM with a system prompt that asks it to summarize each file in a compact way, and writes the result back out to the tree.

The ugly XML tag is to avoid conflicts. Some other scripts try to make a Markdown document of the tree which is silly because your tree is quite likely to contain Markdown already, and so it's confusing for the model to see ``` that doesn't really terminate the block. Using a marker pattern that's unlikely to occur in your code fixes that.