Quote from Thanks! I've been looking to install some Beta mods and the newer launcher just doesn't work with mods before 1.0.0. I don't know why.

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But this really helped! Now I can make the mod-pack of my dreams! In order to manually install mods with the current launcher (this goes for Forge mods as well, when Forge did not have an installer, and Optifine) you have to rename the version you are modding, e.g. From 1.9 to 1.9_mods, including the folder, jar, json, and the 'id' inside the json - as well as; otherwise, the steps should be the same. The Wiki has more detailed steps, although simply renaming the jar to zip and extracting it with Windows's built-in zip utility will not work for many older jars, since they have a file named 'aux.class', which is an illegal filename (I use WinRar to mod the jar), and they do not mention the need to delete the 'downloads' section from the json file, which was added a few weeks ago and causes the launcher to redownload the jar even if it has been renamed.