Disable Command-M to minimize window

You can disable it by editing ~/Library/Preferences/.GlobalPreferences.plist:

defaults write -g NSUserKeyEquivalents -dict-add 'Minimize' '\0'

To apply the changes you have to reopen applications. If the shortcut was assigned to nil, pressing L would trigger it in Audacity.

You can "override" the default Command-M shortcut by mapping it to something else. To remap the key combination, launch System Preferences and choose Keyboard. Then the Keyboard Preferences Panel appears, click on the right tab named "Keyboard Shortcuts". You will notice many default keyboard shortcuts that you can override.

I've tried remapping Command-M using this method and it works.

Remapping Command-M to Zoom in "All Applications" seemed to be a good workaround as Zoom appears in all applications and doesn't have nearly as disruptive an effect as an unintentional Minimize.

I was going to try the terminal command above so I went to remove the command M for Zoom and lo and behold, Minimize was now listed with no key command. So I just left it that way, now command-M does nothing and minimize lives harmlessly in the Menu. No terminal command necessary.

You can remap any key and key combination with the wonderful and free software Karabiner. After installing, just add the following code to your ~/Library/Application Support/Karabiner/private.xml:

  <item>
    <name>Map Cmd-M to Cmd-Alt-M</name>
    <appendix>Changes the minimize shortcut</appendix>
    <not>EMACS</not>
    <identifier>private.kill_m</identifier>
    <autogen>__KeyToKey__ KeyCode::M, ModifierFlag::COMMAND_L|ModifierFlag::OPTION_L, KeyCode::M, ModifierFlag::COMMAND_L</autogen>
    <autogen>__KeyToKey__ KeyCode::M, ModifierFlag::COMMAND_L, KeyCode::VK_NONE</autogen>
  </item>

  <item>
    <name>Map Cmd-Q to Cmd-Alt-Q</name>
    <appendix>Changes the quit shortcut</appendix>
    <not>EMACS</not>
    <identifier>private.kill_q</identifier>
    <autogen>__KeyToKey__ KeyCode::Q, ModifierFlag::COMMAND_L|ModifierFlag::OPTION_L, KeyCode::Q, ModifierFlag::COMMAND_L</autogen>
    <autogen>__KeyToKey__ KeyCode::Q, ModifierFlag::COMMAND_L, KeyCode::VK_NONE</autogen>
  </item>

Then klick "Reload XML" in the Karabiner preferences and set checkmarks for the new items.

This way the minimizing shortcut is not entirely disabled but still available with the additional option key: Cmd+Option+M or by simply using the right command key: Cmd (right)+M.

Note that the second part also changes the Cmd+Q shortcut to Cmd+Option+Q for your convenience. You can omit the second item, if you don’t need it.