Some files missing after database creation

While trying to create a database for the [fuchsia operating system](https://fuchsia.dev), it seems to leave out some of the files that were built.

Note that the steps to build fuchsia and a codeql database require ~200GB of disk space. I just want to get a better understanding of why it might be skipping some of the files.

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Steps to reproduce:

1. Follow steps on the fuchsia site to [download an build fuchsia](https://fuchsia.dev/fuchsia-src/getting_started)
1. Inside the fuchsia directory, run: `fx set workstation.x64 --with-base //bundles:kitchen_sink --no-goma `
1. Build the database: `codeql database create fuchsia-ql --language=cpp --source-root=${FUCHSIA_DIR} --command="./scripts/fx clean-build"`
1. List the files with a script similar to [this one](https://github.com/github/codeql-cli-binaries/issues/13#issue-554520733)
1. List all the fuchsia cc, ignoring the third_party files: `find ${FUCHSIA_DIR} -iname "*.cc" | grep -v "third_party"`
1. Compare the files in the database with the cc files. Some of the files are missing.

[This is the list](https://www.irccloud.com/pastebin/raw/6mk596gp) that I have in my system. In particular, files like `/zircon/tools/zbi/zbi.cc` should always be built.

To get a list of all the compiled files in fuchsia, run: `fx compdb` and then look at `out/default/compile_commands.json` and `out/default.zircon/compile_commands.json`

Reproduce the database with the Fuchsia build steps and the `codeql database create` command in the issue. Compare the database contents with `out/default/compile_commands.json`, `out/default.zircon/compile_commands.json`, and the `find` results, checking the reported `/zircon/tools/zbi/zbi.cc` case. Done means identifying why compiled files are omitted and documenting or fixing the extraction behavior.

Written by the indexing model from the issue text.