Fix SBC overlay upgrade + simplify PCIe Gen 3 config

Two fixes in one:

1. SBC overlay upgrade path: the overlay installer was always writing
   to /boot/EFI, but on SBC layouts (no BOOT partition) the GRUB code
   mounts EFI at /boot. Config.txt and firmware ended up in a stale
   /boot/EFI/ subdirectory, invisible to the firmware. The installer
   now detects the SBC layout and writes to the correct location.

2. PCIe Gen 3: dtparam=pciex1_gen=3 works on CM5 (the DT overrides
   exist), so the custom pcie-gen3.dtbo overlay is unnecessary.
   Simplified to just use dtparam in config.txt.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

config/config.txt

@@ -18,9 +18,7 @@ enable_uart=1
 [pi5]
 enable_uart=0
 # Enable PCIe Gen 3 for NVMe (~800 MB/s vs ~400 MB/s Gen 2)
-# CM5 DTB lacks the pciex1 alias needed for dtparam=pciex1_gen=3,
-# so we use a custom overlay that targets pcie@1000110000 directly.
-dtoverlay=pcie-gen3
+dtparam=pciex1_gen=3
 [all]
 # Disable Bluetooth.
 dtoverlay=disable-bt

patches/talos-rpi5/sbc-raspberrypi5/0003-Add-PCIe-Gen-3-overlay-for-CM5.patch

@@ -1,66 +0,0 @@
-From b7b424db9b0f771c60c4090c30bf1246eeef6995 Mon Sep 17 00:00:00 2001
-From: Mathias Beaulieu-Duncan <mathias@openharbor.io>
-Date: Mon, 16 Feb 2026 19:07:45 -0500
-Subject: [PATCH] Add PCIe Gen 3 overlay for CM5
-
-The CM5 device tree (bcm2712-rpi-cm5-cm5io.dtb) lacks the pciex1 alias
-that the Pi 5 DTB provides, making dtparam=pciex1_gen=3 silently
-non-functional on CM5 boards.
-
-This adds a custom device tree overlay (pcie-gen3.dtbo) that targets
-/axi/pcie@1000110000 directly to set max-link-speed = <3>, bypassing
-the missing alias entirely. The overlay is embedded in the installer
-binary and written to /boot/EFI/overlays/ during install/upgrade.
-
-Combined with dtoverlay=pcie-gen3 in config.txt, this enables PCIe
-Gen 3 (8.0 GT/s, ~800 MB/s) for NVMe on CM5 Compute Blades.
----
- installers/rpi5/src/main.go        |  10 ++++++++++
- installers/rpi5/src/pcie-gen3.dtbo | Bin 0 -> 230 bytes
- 2 files changed, 10 insertions(+)
- create mode 100644 installers/rpi5/src/pcie-gen3.dtbo
-
-diff --git a/installers/rpi5/src/main.go b/installers/rpi5/src/main.go
-index fed3819..1134168 100644
---- a/installers/rpi5/src/main.go
-+++ b/installers/rpi5/src/main.go
-@@ -17,6 +17,9 @@ import (
- //go:embed config.txt
- var configTxt []byte
- 
-+//go:embed pcie-gen3.dtbo
-+var pcieGen3Dtbo []byte
-+
- func main() {
- 	adapter.Execute(&RpiInstaller{})
- }
-@@ -52,6 +55,13 @@ func (i *RpiInstaller) Install(options overlay.InstallOptions[rpiOptions]) error
- 		return err
- 	}
- 
-+	// Write custom PCIe Gen 3 overlay for CM5 (its DTB lacks the pciex1 alias
-+	// needed by dtparam, so we target pcie@1000110000 directly).
-+	err = os.WriteFile(filepath.Join(options.MountPrefix, "/boot/EFI/overlays/pcie-gen3.dtbo"), pcieGen3Dtbo, 0o644)
-+	if err != nil {
-+		return err
-+	}
-+
- 	if options.ExtraOptions.ConfigTxt != "" {
- 		configTxt = []byte(options.ExtraOptions.ConfigTxt)
- 	}
-diff --git a/installers/rpi5/src/pcie-gen3.dtbo b/installers/rpi5/src/pcie-gen3.dtbo
-new file mode 100644
-index 0000000000000000000000000000000000000000..863d0ea1bd8860dd361fe12d017330655d97a39e
-GIT binary patch
-literal 230
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-literal 0
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--- 
-2.50.1 (Apple Git-155)
-

patches/talos-rpi5/sbc-raspberrypi5/0003-Fix-SBC-overlay-upgrade-detect-EFI-mount-path-for-SB.patch

@@ -0,0 +1,67 @@
+From 113b5acba0bfc2fcc4f7494f88b0b9601bdbd4c2 Mon Sep 17 00:00:00 2001
+From: Mathias Beaulieu-Duncan <mathias@openharbor.io>
+Date: Mon, 16 Feb 2026 19:07:45 -0500
+Subject: [PATCH] Fix SBC overlay upgrade: detect EFI mount path for SBC
+ layouts
+MIME-Version: 1.0
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+
+On SBC platforms (RPi5/CM5), the disk layout has no separate BOOT
+partition. During upgrades, the GRUB install code mounts the EFI
+partition at /boot instead of /boot/EFI. The overlay installer was
+always writing to /boot/EFI, causing config.txt and firmware files
+to end up in the wrong subdirectory — invisible to the firmware.
+
+Detect the SBC layout by checking if config.txt already exists at
+/boot/ (indicating EFI is mounted there), and write files to the
+correct location. Also clean up any stale /boot/EFI/ directory
+from previous incorrect upgrades.
+---
+ installers/rpi5/src/main.go | 22 +++++++++++++++++-----
+ 1 file changed, 17 insertions(+), 5 deletions(-)
+
+diff --git a/installers/rpi5/src/main.go b/installers/rpi5/src/main.go
+index fed3819..862d72e 100644
+--- a/installers/rpi5/src/main.go
++++ b/installers/rpi5/src/main.go
+@@ -42,13 +42,25 @@ func (i *RpiInstaller) GetOptions(extra rpiOptions) (overlay.Options, error) {
+ }
+ 
+ func (i *RpiInstaller) Install(options overlay.InstallOptions[rpiOptions]) error {
+-	err := copy.Dir(filepath.Join(options.ArtifactsPath, "arm64/firmware/boot"), filepath.Join(options.MountPrefix, "/boot/EFI"))
+-	if err != nil {
++	// Determine where the EFI partition is mounted.
++	// Standard layout: BOOT (XFS) at /boot, EFI (VFAT) at /boot/EFI
++	// SBC layout:      no BOOT partition, EFI (VFAT) at /boot
++	efiDir := filepath.Join(options.MountPrefix, "/boot/EFI")
++
++	if _, err := os.Stat(filepath.Join(options.MountPrefix, "/boot/config.txt")); err == nil {
++		// config.txt exists at /boot — EFI partition is mounted at /boot (SBC layout).
++		efiDir = filepath.Join(options.MountPrefix, "/boot")
++
++		// Clean up stale /boot/EFI/ directory from previous upgrades that
++		// wrote to the wrong path.
++		os.RemoveAll(filepath.Join(options.MountPrefix, "/boot/EFI"))
++	}
++
++	if err := copy.Dir(filepath.Join(options.ArtifactsPath, "arm64/firmware/boot"), efiDir); err != nil {
+ 		return err
+ 	}
+ 
+-	err = copy.File(filepath.Join(options.ArtifactsPath, "arm64/u-boot/rpi5/u-boot.bin"), filepath.Join(options.MountPrefix, "/boot/EFI/u-boot.bin"))
+-	if err != nil {
++	if err := copy.File(filepath.Join(options.ArtifactsPath, "arm64/u-boot/rpi5/u-boot.bin"), filepath.Join(efiDir, "u-boot.bin")); err != nil {
+ 		return err
+ 	}
+ 
+@@ -58,5 +70,5 @@ func (i *RpiInstaller) Install(options overlay.InstallOptions[rpiOptions]) error
+ 
+ 	configTxt = append(configTxt, []byte("\n"+options.ExtraOptions.ConfigTxtAppend)...)
+ 
+-	return os.WriteFile(filepath.Join(options.MountPrefix, "/boot/EFI/config.txt"), configTxt, 0o644)
++	return os.WriteFile(filepath.Join(efiDir, "config.txt"), configTxt, 0o644)
+ }
+-- 
+2.50.1 (Apple Git-155)
+