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An external tool cannot operate on files 'down' from a project root if there are any linked folders, since it has no way of expanding the linked folder name. The only method is to explicitly state linked folder names as ${} variables in the tool command line, which then makes the tool definitions project-specific, somewhat defeating the object. It would be useful if there was a mechanism to allow an external tool to do this expansion.
I'm still not quite following. Are you talking about expanding linked folders that are provided as arguments to an external tool (In Run > External Tools > External Tool... dialog)?
Closing. Requested details not provided.
Thought was to provide 'variables' that could be used in the tools command line that would be expanded in the same way as those used in e.g. the Project Build settings, to refer to workspace- and project-relative resources.
Scratch #3, I wasn't thinking clearly ! Say you want to set up an external tool to Lint a project. The project may contain linked subfolders as well as 'normal' ones. From the Eclipse project point of view, you can just navigate down the hierarchy if you want to refer to any file in a subdirectory. However if you want to run a tool on the project, the tool cannot just go down the hierarchy since when it hits a linked folder it cannot resolve it - that depends on Eclipse's knowledge. The only way I could come up with would be to (temporarily?) insert symbolic links into the project directory structure to point to the linked resources - then the tool would be unaware of any difference between linked and normal folders. But this is a kludge. So I was soliciting views on how else you might acheive the required result, i.e. running useful external tools on projects containing linked folders. A magic tool-runner app akin to fakeroot, that ran the external tool and made the linked folders appear to be real ?
Reopening due to response. I don't have an answer on hand, but I'll keep this open to track discussion.
This bug hasn't had any activity in quite some time. Maybe the problem got resolved, was a duplicate of something else, or became less pressing for some reason - or maybe it's still relevant but just hasn't been looked at yet. If you have further information on the current state of the bug, please add it. The information can be, for example, that the problem still occurs, that you still want the feature, that more information is needed, or that the bug is (for whatever reason) no longer relevant.