Markdown is excellent for focused and productive writing, but it might occasionally interfere with the specifics of your writing task. If you're using a Mac, you can customize the markup to better suit your needs.

Let's assume you need to use the [square brackets] without Ulysses marking them as links. In this case, you can escape this by adding a backslash before the opening tag. In our example, this would look like this: \[square brackets]. However, you'll probably find it inconvenient to do it over and over again. The alternative is to adjust the Link markup.

To customize your markup, go to Ulysses › Settings… and switch to the "Markup" tab. Now, click on the pop-up button of the markup selection in the top left-hand corner and select "New Markup."

Choose a name for your new markup and select a template to use as a basis. For now, let's stick to Ulysses' default markup language, Markdown XL.

Once this is done, scroll down to the Link markup in the definitions overview and double-click it. You can now modify the Link tag. Enter, for example, angular brackets < > instead of square brackets or switch to double square brackets [[ ]] – choose whatever suits you best.

Finally, select the sheets to which you would like to apply the new markup and go to Edit › Convert Markup to select your markup.

While you can only create a new markup on a Mac, it also synchronizes to your iOS devices via iCloud. To apply the markup there, open the "Editor Settings" via the circled ellipsis in a sheet. Under "Markup," you can select the newly created markup. 

From now on, square brackets will no longer be treated as links when this markup is selected. Instead, angled brackets (or whatever you have replaced them with) will serve as links. Of course, this can also be applied to other tags within a markup, not just links.

Keep in mind that you'll need to manually update the markup on each individual sheet, as glued sheets won't update automatically. Additionally, all existing links in your sheet will be automatically converted to the new markup.