autotools build-dir handling not compatible with relative conf-root

It was noticed during testing that conf-root is by default ".". When build-dir is set, this results in configure being invoked from wrong directory. A solution needs to take into account that command-subdir might be set (autotools project might be in a subdirectory inside a monorepo).

Start by locating the Python autotools plugin and the code that resolves conf-root, build-dir, and command-subdir. Reproduce the case where conf-root is "." and build-dir is set, including an autotools project in a monorepo subdirectory. Done means configure runs from the correct directory in both layouts.

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