Fix module dependency resolution issues

- Fix dependency resolution to use built modules from /lib/modules/6.12.44-Zero-OS instead of fresh container
- Fix stage1/stage2 configuration mismatch (only using stage1 modules as intended)
- Fix firmware parsing to ignore comments in modules.conf
- Fix variable binding issues for incremental builds (FULL_KERNEL_VERSION, KERNEL_OUTPUT)
- Module resolution now properly expands 31 → 48 modules with dependencies
- Firmware requirements reduced from 157 bogus → 3 correct packages
- All 48/48 resolved modules validated as available .ko files

config/modules.conf

@@ -2,12 +2,14 @@
 # Format: STAGE:MODULE_NAME:FIRMWARE_PACKAGE (optional)
 # Focus on most common NIC modules to ensure networking works on most hardware
 
-# Stage 1: ALL networking and essential boot modules
-# All NICs must be loaded BEFORE network can come up
+# Stage 1: Core subsystems + networking and essential boot modules
+# All core subsystems and NICs must be loaded BEFORE network can come up
+stage1:virtio:none                      # Core virtio subsystem (REQUIRED)
+stage1:virtio_ring:none                 # Virtio ring buffer (REQUIRED)
+stage1:virtio_pci:none                  # Virtio PCI bus
 stage1:virtio_net:none                  # Virtio network (VMs, cloud)
 stage1:virtio_scsi:none                 # Virtio SCSI (VMs, cloud)
 stage1:virtio_blk:none                  # Virtio block (VMs, cloud)
-stage1:virtio_pci:none                  # Virtio PCI bus
 stage1:e1000:linux-firmware-intel      # Intel E1000 (very common)
 stage1:e1000e:linux-firmware-intel     # Intel E1000E (very common)
 stage1:r8169:linux-firmware-realtek    # Realtek (most common desktop/server)
@@ -25,9 +27,11 @@ stage1:atl1:none                        # Atheros L1
 stage1:atl1e:none                       # Atheros L1E
 stage1:atl1c:none                       # Atheros L1C
 stage1:alx:none                         # Atheros Alx
+stage1:libata:none                      # Core ATA subsystem (REQUIRED)
 stage1:scsi_mod:none                    # SCSI subsystem
 stage1:sd_mod:none                      # SCSI disk support
 stage1:ahci:none                        # SATA AHCI
+stage1:nvme_core:none                   # Core NVMe subsystem (REQUIRED)
 stage1:nvme:none                        # NVMe storage
 stage1:tun:none                         # TUN/TAP for networking
 stage1:overlay:none                     # OverlayFS for containers