After hunting for over an hour, I found the solution for this in various places.
To summarize, Forge no longer wants you to import mods directly into the .jar file, but to "design them properly" so that it can have control over the way it is imported.
This is fine in concept except that they haven't (yet) provided ANY way to easily import what they refer to as a "coremod".
Take Risagumi's "Death Chest" mod for example.
I put it in the ".minecraft/mods" folder and it simply gets ignored and not imported into minecraft. The log files show that it is scanned, but no mod is found in it.
I put it in the old ".minecraft/coremods" folder (no longer used by Forge and it doesn't even show in the log files.
I add it directly to the ".minecraft/versions/1.6.2-Forge188.8.131.529/1.6.2-Forge184.108.40.2069.jar" file and Forge prevents Minecraft from loading with errors containing "CRITICAL TAMPERING...FML will not launch minecraft".
Anyway, to force Forge to allow the mods to load, you need to do the following:
1. Install Forge according to the directions (using the new Forge installer).
2. Import your "core" mods that aren't loading properly into the .jar file.
3. Remove the META_INF folder from the .jar file before saving and closing it. (Heard it a million times, still forget.)
4. Start Minecraft.
5. Select and Edit the Forge profile.
6. Checkmark the "JVM Arguments" option and add the following items (space between each option): -Dfml.ignorePatchDiscrepancies=true -Dfml.ignoreInvalidMinecraftCertificates=true
7. Click the Save Profile button.
You're good to play.
While this might open you up to "unauthorized" modifications to the core code, until Forge gets a good way to actually import core mods or adds hooks for completely overriding functions and variables in the core classes, this will be necessary for some mods to play nicely with Forge.Forge's suggestion for coremods is now to use Access Transformers: http://www.minecraftforge.net/wiki/Using_Access_Transformers
While this might appear to be a good thing in theory, it's way past what should be necessary if a modder wants to add or change a few lines of code in one of the core files.
P.S.: If I'm wrong, please tell me so and point me to the correct solution--I really hope I'm wrong...
You may be able to load mods into mincraft that mod the jar in a way similar to how I added optifine to forge in my linked thread. you say risugami's death chest? I'll test it.
[EDIT] It is confirmed, I can load DeathChest as a library using the json file.
Steps to replicate:
1. Install forge using the official installer (I reccomend version 220.127.116.119)
2. Copy the forge version in .minecraft/versions and rename it Forge-1.6.2
3. Rename the json and jar inside the forge version to Forge-1.6.2.jar/json
4. Open the json file in notepad (preferably notepad++) or whatever text editor your system has.
5. Change the line
7. Place the deathchest zip in .minecraft/risugami/deathchest/deathchest/1.6.2/, making folders as needed, and name it deathchest-1.6.2.jar (note the change from zip to jar, this must be done.)
8. Open your launcher and create a new profile; tell it to use version Forge-1.6.2 and add "-Dfml.ignorePatchDiscrepancies=true" as a jvm argument (don't forget a space " " between arguements)
9. Play with forge and Death Chest!
yeah weird also thank you your problem allowed me to see what i was doing wrong because i forgot to add the line -Dfml.ignorePatchDiscrepancies=true -Dfml.ignoreInvalidMinecraftCertificates=true thanks