Bug 25387 [Wizards] [resources] File System Import changes file permissions
Creating a Project (simple or otherwise) and importing files into it using the import->File System wizard takes away the executable permission from the imported exec files.
bundles/org.eclipse.ui.ide/src/org/eclipse/ui/wizards/datatransfer/ImportOperation.java
if (overwriteAnswer.equals(IOverwriteQuery.NO)) {
            return false;
        }
        if (overwriteAnswer.equals(IOverwriteQuery.NO_ALL)) {
            this.overwriteState = OVERWRITE_NONE;
            return false;
        }
        if (overwriteAnswer.equals(IOverwriteQuery.ALL))
            this.overwriteState = OVERWRITE_ALL;
        return true;
    }
    /**
     * Returns whether the given file should be overwritten.
     *
     * @param targetFile the file to ask to overwrite 
     * @param policy determines if the user is queried for overwrite 
     * @return <code>true</code> if the file should be overwritten, and
     * 	<code>false</code> if not.
     */
    boolean queryOverwriteFile(IFile targetFile, int policy) {
        
        if (policy != POLICY_FORCE_OVERWRITE) {
            if (this.overwriteState == OVERWRITE_NOT_SET
                    && !queryOverwrite(targetFile.getFullPath()))
                return false;
            if (this.overwriteState == OVERWRITE_NONE)
                return false;
        }
        return true;
    }