I assume that you are using the official launcher to try running a modded version and it isn't working? You can't just add some files to the jar because the launcher will think it is corrupted and redownload it unless you make a copy of the version that you want to modify (e.g. "versions\1.12.2" to "versions\1.12.2_modded"), then rename it as well as the jar and json files inside. Then, you need to open the json file and look for "client.jar" (no quotes) and delete the entire "downloads" section that encloses it, and also edit the following "id": "1.12.2" line to match the name you used before:
Before (the downloaded jsons are not formatted with line breaks):
If you have some other issue, I'm not sure why MCP wouldn't be producing the reobfuscated files; you didn't happen to update the MD5s? This will mark all files as unmodified; otherwise, I only use MCP itself by directly running the batch files that come with it, not Eclipse, but some command might be incorrect, or you put your source files in the wrong location (I put them in with the vanilla files, in addition to any modified vanilla classes, and the package I use is "net.minecraft.src" (1.6.4, which might be different for 1.12.2 since they use separate folders for everything since 1.7).