I build the newest version by cloning the repository into ProjectRed and running ant in it. Then I took the jars from /dist/1.6.2/4.0.0-0/ and got this error on startup:
---- Minecraft Crash Report ----
// Would you like a cupcake?

Time: 9/4/13 7:54 PM
Description: Initializing game

java.lang.NoClassDefFoundError: mrtjp/projectred/ProjectRedCore$1
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:339)
at cpw.mods.fml.common.FMLModContainer.constructMod(FMLModContainer.java:457)
at sun.reflect.GeneratedMethodAccessor2.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:491)
at com.google.common.eventbus.EventHandler.handleEvent(EventHandler.java:74)
at com.google.common.eventbus.SynchronizedEventHandler.handleEvent(SynchronizedEventHandler.java:45)
at com.google.common.eventbus.EventBus.dispatch(EventBus.java:313)
at com.google.common.eventbus.EventBus.dispatchQueuedEvents(EventBus.java:296)
at com.google.common.eventbus.EventBus.post(EventBus.java:267)
at cpw.mods.fml.common.LoadController.sendEventToModContainer(LoadController.java:194)
at cpw.mods.fml.common.LoadController.propogateStateMessage(LoadController.java:174)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:491)
at com.google.common.eventbus.EventHandler.handleEvent(EventHandler.java:74)
at com.google.common.eventbus.SynchronizedEventHandler.handleEvent(SynchronizedEventHandler.java:45)
at com.google.common.eventbus.EventBus.dispatch(EventBus.java:313)
at com.google.common.eventbus.EventBus.dispatchQueuedEvents(EventBus.java:296)
at com.google.common.eventbus.EventBus.post(EventBus.java:267)
at cpw.mods.fml.common.LoadController.distributeStateMessage(LoadController.java:105)
at cpw.mods.fml.common.Loader.loadMods(Loader.java:509)
at cpw.mods.fml.client.FMLClientHandler.beginMinecraftLoading(FMLClientHandler.java:181)
at net.minecraft.client.Minecraft.func_71384_a(Minecraft.java:470)
at net.minecraft.client.Minecraft.func_99999_d(Minecraft.java:796)
at net.minecraft.client.main.Main.main(SourceFile:101)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:491)
at net.minecraft.launchwrapper.Launch.launch(Launch.java:57)
at net.minecraft.launchwrapper.Launch.main(Launch.java:18)
Caused by: java.lang.ClassNotFoundException: mrtjp.projectred.ProjectRedCore$1
at net.minecraft.launchwrapper.LaunchClassLoader.findClass(LaunchClassLoader.java:179)
at java.lang.ClassLoader.loadClass(ClassLoader.java:423)
at java.lang.ClassLoader.loadClass(ClassLoader.java:356)
... 34 more
Caused by: java.lang.NullPointerException
at net.minecraft.launchwrapper.LaunchClassLoader.findClass(LaunchClassLoader.java:171)
... 36 more

A detailed walkthrough of the error, its code path and all known details is as follows:

-- Head --
Stacktrace:
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:339)
at cpw.mods.fml.common.FMLModContainer.constructMod(FMLModContainer.java:457)
at sun.reflect.GeneratedMethodAccessor2.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:491)
at com.google.common.eventbus.EventHandler.handleEvent(EventHandler.java:74)
at com.google.common.eventbus.SynchronizedEventHandler.handleEvent(SynchronizedEventHandler.java:45)
at com.google.common.eventbus.EventBus.dispatch(EventBus.java:313)
at com.google.common.eventbus.EventBus.dispatchQueuedEvents(EventBus.java:296)
at com.google.common.eventbus.EventBus.post(EventBus.java:267)
at cpw.mods.fml.common.LoadController.sendEventToModContainer(LoadController.java:194)
at cpw.mods.fml.common.LoadController.propogateStateMessage(LoadController.java:174)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:491)
at com.google.common.eventbus.EventHandler.handleEvent(EventHandler.java:74)
at com.google.common.eventbus.SynchronizedEventHandler.handleEvent(SynchronizedEventHandler.java:45)
at com.google.common.eventbus.EventBus.dispatch(EventBus.java:313)
at com.google.common.eventbus.EventBus.dispatchQueuedEvents(EventBus.java:296)
at com.google.common.eventbus.EventBus.post(EventBus.java:267)
at cpw.mods.fml.common.LoadController.distributeStateMessage(LoadController.java:105)
at cpw.mods.fml.common.Loader.loadMods(Loader.java:509)
at cpw.mods.fml.client.FMLClientHandler.beginMinecraftLoading(FMLClientHandler.java:181)
at net.minecraft.client.Minecraft.func_71384_a(Minecraft.java:470)

-- Initialization --
Details:
Stacktrace:
at net.minecraft.client.Minecraft.func_99999_d(Minecraft.java:796)
at net.minecraft.client.main.Main.main(SourceFile:101)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:491)
at net.minecraft.launchwrapper.Launch.launch(Launch.java:57)
at net.minecraft.launchwrapper.Launch.main(Launch.java:18)

-- System Details --
Details:
Minecraft Version: 1.6.2
Operating System: Linux (amd64) version 3.10-2-amd64
Java Version: 1.8.0-ea, Oracle Corporation
Java VM Version: Java HotSpot(TM) 64-Bit Server VM (mixed mode), Oracle Corporation
Memory: 128781384 bytes (122 MB) / 469237760 bytes (447 MB) up to 954728448 bytes (910 MB)
JVM Flags: 1 total; -Xmx1G
AABB Pool Size: 0 (0 bytes; 0 MB) allocated, 0 (0 bytes; 0 MB) used
Suspicious classes: FML and Forge are installed
IntCache: cache: 0, tcache: 0, allocated: 0, tallocated: 0
FML: MCP v8.04 FML v6.2.57.845 Minecraft Forge 9.10.0.845 Optifine OptiFine_1.6.2_HD_U_C1 67 mods loaded, 67 mods active
mcp{8.04} Minecraft Coder Pack Unloaded->Constructed
FML{6.2.57.845} Forge Mod Loader Unloaded->Constructed
Forge{9.10.0.845} Minecraft Forge Unloaded->Constructed
CodeChickenCore{0.9.0.5} CodeChicken Core Unloaded->Constructed
NotEnoughItems{1.6.1.3} [Not Enough Items](NotEnoughItems 1.6.1.3.jar) Unloaded->Constructed
AppliedEnergistics-Core{rv13.b} AppliedEnergistics Core Unloaded->Constructed
IC2{2.0.128-experimental} IndustrialCraft 2 Unloaded->Constructed
AdvancedMachines{5.1.7} IC2 Advanced Machines Addon Unloaded->Constructed
AtomicScience{0.7.1} Atomic Science Unloaded->Constructed
Natura{2.1.7} Natura Unloaded->Constructed
BiomesOPlenty{0.6.2} Biomes O' Plenty Unloaded->Constructed
ChickenChunks{1.3.3.2} [ChickenChunks](ChickenChunks 1.3.3.2.jar) Unloaded->Constructed
complexmachines{0.3.3} Complex Machines Unloaded->Constructed
ComputerCraft{1.56} ComputerCraft Unloaded->Constructed
CCTurtle{1.56} ComputerCraft Turtles Unloaded->Constructed
EnderStorage{1.4.3.3} [EnderStorage](EnderStorage 1.4.3.3.jar) Unloaded->Constructed
Forestry{2.3.0.1} Forestry for Minecraft Unloaded->Constructed
factorization{0.8.04beta2} Factorization Unloaded->Constructed
BuildCraft|Core{4.0.2} BuildCraft Unloaded->Constructed
BuildCraft|Builders{4.0.2} BC Builders Unloaded->Constructed
BuildCraft|Energy{4.0.2} BC Energy Unloaded->Constructed
BuildCraft|Factory{4.0.2} BC Factory Unloaded->Constructed
Railcraft{8.0.1.0} Railcraft Unloaded->Constructed
DartCraft{Beta 0.2.05} [DartCraft](DartCraft Beta 0.2.05.jar) Unloaded->Constructed
EnderIO{0.1.15} Ender IO Unloaded->Constructed
factorization.misc{0.8.04beta2} Factorization Miscellaneous Nonsense Unloaded->Constructed
factorization.notify{0.8.04beta2} Factorization Notification System Unloaded->Constructed
factorization.dimensionalSlice{0.8.04beta2} Factorization Dimensional Slices Unloaded->Constructed
ForgeMultipart{1.0.0.153} Forge Multipart Unloaded->Constructed
McMultipart{1.0.0.153} Minecraft Multipart Plugin Unloaded->Constructed
mod_Gammabright{by kymaster, v2.0 for MC 1.6.2} [mod_Gammabright](Gammabright v2.0 [MC 1.6.2].zip) Unloaded->Constructed
Hats{2.0.1} Hats Unloaded->Constructed
ICBM|Contraption{1.3.2} ICBM|Contraption Unloaded->Constructed
ICBM|Sentry{1.3.2} ICBM|Sentry Unloaded->Constructed
ICBM|Explosion{1.3.2} ICBM|Explosion Unloaded->Constructed
MFFS{3.3.1} Modular Force Field System Unloaded->Constructed
Mekanism{5.5.7} Mekanism Unloaded->Constructed
MekanismGenerators{5.5.7} MekanismGenerators Unloaded->Constructed
MekanismTools{5.5.7} MekanismTools Unloaded->Constructed
powersuits{0.8.0-646} MachineMuse's Modular Powersuits Unloaded->Constructed
Morph{0.1.0} Morph Unloaded->Constructed
NaturalBiomes2{0.5.4} [Natural Biomes 2](NB2 1.6.2 v0.5.4.zip) Unloaded->Constructed
Natura|CompatMineFactoryReloaded{0.1} Natura compat: MFR Unloaded->Constructed
iChunUtil{2.1.0} iChunUtil Unloaded->Constructed
PortalGun{2.0.0} PortalGun Unloaded->Constructed
ProjRed|Core{4.0.0.0} Project: Red-Core Unloaded
JAKJ_RedstoneInMotion{2.0.0.0} Redstone In Motion Unloaded
resonantinduction{0.2.0} Resonant Induction Unloaded
StevesCarts{2.0.0.a132} Steve's Carts 2 Unloaded
TConstruct{1.6.2_1.4.3} Tinkers' Construct Unloaded
TConstruct|CompatMineFactoryReloaded{0.1} TConstruct Compat: MFR Unloaded
Translocator{1.1.0.8} [Translocator](Translocator 1.1.0.8.jar) Unloaded
TrussMod{beta} Truss Mod Unloaded
mod_ZanMinimap{Not available} mod_ZanMinimap Unloaded
AppliedEnergistics{rv13.b} Applied Energistics Unloaded
BinnieCore{1.8-dev1} Binnie Core Unloaded
ExtraBees{1.8-dev1} Extra Bees Unloaded
ExtraTrees{1.8-dev1} Extra Trees Unloaded
BuildCraft|Transport{4.0.2} BC Transport Unloaded
BuildCraft|Silicon{4.0.2} BC Silicon Unloaded
CompactSolars{4.4.12.120} Compact Solar Arrays Unloaded
ExtraUtilities{0.3 prerelease 3a} [Extra Utilities](extrautils - 0.3 Prerelease 3a.zip) Unloaded
IronChest{5.3.20.547} Iron Chest Unloaded
MiscPeripherals{3.3} MiscPeripherals Unloaded
Mystcraft{0.10.6.00} Mystcraft Unloaded
BasicComponents{1.0.0} Basic Components Unloaded
ForgeMicroblock{1.0.0.153} Forge Microblocks Unloaded
Launched Version: 1.6.2-Forge9.10.0.845
LWJGL: 2.9.0
OpenGL: GeForce 7600 GT/PCIe/SSE2 GL version 2.1.2 NVIDIA 304.108, NVIDIA Corporation
Is Modded: Definitely; Client brand changed to 'fml,forge'
Type: Client (map_client.txt)
Resource Pack: Default
Current Language: English (UK)
Profiler Position: N/A (disabled)
Vec3 Pool Size: ERROR NullPointerException: null

The line before this error in the ForgeModLoader-client-0.log is:
2013-09-04 19:54:53 [FINEST] [ProjRed|Core] Sending event FMLConstructionEvent to mod ProjRed|Core

Its not including all the files during obfuscation. The build script should do it all for you, so if its not working, its most likely a system config error. Look elsewhere for common errors related to MCP, Forge installation, reobfuscation and such. Though, you shouldn't even need to compile. Just run a debug instance from eclipse, and you should be able to test out any code changes you made.