Bug Report

• Yes, I reviewed the contribution guidelines.
• Yes, more specifically, I reviewed the guidelines on how to write clear bug reports.

Describe the current, buggy behavior

Package is only very partially overridden by classes from a locally installed version of the package (classes from ~/.wp-cli/packages/vendor/wp-cli/export-command)

Describe how other contributors can replicate this bug

sudo curl -sLo wp https://github.com/wp-cli/wp-cli/.../wp-cli-1.5.0.phar && chmod +x ./wp
wp package install https://github.com/wp-cli/export-command.git ## <---- We override export-command
./wp eval "var_dump((new \ReflectionClass('\WP_Export_WXR_Formatter'))->getFileName(),
                    (new \ReflectionClass('\Export_Command'))->getFileName());"

Actual result

phar://./wp/vendor/wp-cli/export-command/src/WP_Export_WXR_Formatter.php
~/.wp-cli/packages/vendor/wp-cli/export-command/src/Export_Command.php

Desired result

~/.wp-cli/packages/vendor/wp-cli/export-command/src/WP_Export_WXR_Formatter.php
~/.wp-cli/packages/vendor/wp-cli/export-command/src/Export_Command.php