How is the final config assembled if I have multiple configfiles (eg

PANTS_CONFIG_FILES=pants.ci.toml

in addition to pants.toml). Say I have in both files a section

[blah]

. Does "[blah] from ci.toml" completely overrides the default's [blah] or does some smart merging of config entries happen?

A section in pants.ci.toml does not override a whole section in pants.toml. This happens for each key individually, and depends on its type. If it's a scalar, the later value overwrites the earlier one. If it's a list or dict, the later value can append to the earlier one, or overwrite it, depending on the syntax you use. See here for details