XML files

app config.xml

$PROJECT/www/config.xml

platform config.xml

$PROJECT/platforms/<platform>/.../config.xml (or $NATIVEPROJECT/.../config.xml for Plugman-only).

accidental dummy platform config.xml

$PROJECT/platforms/<platform>/.../www/config.xml

defaults for platform config.xml

$PROJECT/platforms/<platform>/.../defaults.xml

Plugin plugin.xml

$SOMEPLUGIN/plugin.xml

Other metadata files

Installed Plugins and dependencies for platform json

$PROJECT/plugins/<platform>.json

Project config.json

$PROJECT/.cordova/config.json

Cordova user config.json

$HOME/.cordova/config.json

Cordova Plugman user config

$HOME/.plugman/config

Not Documented

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From summary of research by Braden and Anis