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At the moment phpdocumentor only supports one root directory. As a work around I think you should be able to run phpdocumentor from the common root directory of both projects.
we did change a lot in the path handling. So your setup could work.
As in phpDoc v2 paths are relative to the current working directory, but indifference we do only support 1 root directory. at the moment. More about this is explained in #2159
So running phpdocumentor in a directory like this: /opt/phpdoc/src/phpDocumentor/Parser$ ../../../bin/phpdoc --env=dev -d . -d ../Pipeline/ will not work currently.
What phpdocumentor will do is get the first path as "project root". but since ../Pipeline is breaking out of this root it will fail to find the directory. However when you pass a config file:
Expected Behavior
I have two related projects, and I want to include docs generated from both in one run. (Two directories)
Actual Behavior
I only get docs from only one directory.
Steps to Reproduce the Problem
php /will/bin/phpDocumentor2/build/phpDocumentor.phar -d src,../MaxMind-DB-Reader-php/src --cache-folder=mycache -t doc-test
I also tried using a config - same result. Config:
Your environment
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