`compile_commands.json` generated by `compdb` has wrong `command`.

[WeiHe1991]

Hey! Here is a minimal reproducible example, where the compile_commands.json file generated by the tool compdb looks like:

[
    {
        "command": "/usr/bin/g++ -c -I . main.cc --std=c++11 -g3 -pipe -DDEBUG -Wall -Werror -fPIC",
        "directory": "<project_dir>/plz-out/gen",
        "file": "<project_dir>/main.cc"
    }
]

There are currently two issues:

Issue 1

In command, the path to the cc file is a relative one (main.cc in this case). This path, however, expands to <project_dir>/plz-out/gen/main.cc, which does not exist. If you run Clang tools such as clang-tidy against the source file, you'll get an error like:

clang-tidy main.cc               
Error while processing <project_dir>/main.cc.
error: no input files [clang-diagnostic-error]
error: no such file or directory: 'main.cc' [clang-diagnostic-error]
error: unable to handle compilation, expected exactly one compiler job in '' [clang-diagnostic-error]
Found compiler error(s).

IIUC this is due to please by design compiling each translation unit in a temporary directory plz-out/tmp/... using the source file copied into it, instead of the one in the source tree.

Issue 2

This command string is missing include paths. I would expect it to contain -isystem lib/include. Without it Clang tools won't work.

What I also noticed was that the query result from plz query graph (see attached file) is already missing include paths.
plz_query_graph.json

Is there already any workaround to mitigate this issue? If not, I would be happy to contribute.