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I have the documentation for a library accessible as a linked folder (with the value attached to a path variable) within a project. I want to associate the JAR file with the documentation directory, but the options for Javadoc Location in the file Properties are: (1) a directory URL, or (2) a JAR/ZIP file (either external or within the workspace. There is no way to specify a directory within the workspace. Using a file:// URL with an absolute pathname would defeat the purpose of the linked folder. Perhaps there are "workspace URLs" (the example URL "file:/c:/myworkspace/myproject/doc" would seem to imply otherwise), but the UI provides no way for the user to build one by browsing the workspace. There's no user-visible reason there should be any distinction between a folder and an archive for the purposes of attaching documentation to a library.
Indeed we don't support workspace relative URLs for javadoc.