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I have Pathologic installed and it is working great from normal links in a document, but for anything that points to the file system ( img src for example) I can't get it to not use ?q= in the url.

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You could alternatively use the scanner module or export the DB and use a text editor to replace the domains. Therefore getting rid of pathologic.

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If you know how to write a custom module, you can implement hook_pathologic_alter() and tell Pathologic to not modify certain paths. See pathologic.api.php for examples.

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