The BBB seems to auto-detect if an SD is loaded and boots from there; 
otherwise it boots from eMMC, at least mine does.
So I have modified /boot/uboot/uEnv.txt while running on the SD to start up 
with HDMI disabled and PWM and UART1 enabled:









































*root@debian:~# cat 
/boot/uboot/uEnv.txtkernel_file=zImageinitrd_file=initrd.imginitrd_high=0xfffffffffdt_high=0xffffffff#Video:
 
Uncomment to override:#kms_force_mode=video=HDMI-A-1:1024x768@60##Enable 
systemd#systemd=quiet init=/lib/systemd/systemd##BeagleBone Cape 
Overrides##Note: On the BeagleBone Black, there is also an uEnv.txt in the 
eMMC, so if these changes do not seem to be makeing a 
difference...##BeagleBone Black:##Disable 
HDMI/eMMC#optargs=capemgr.disable_partno=BB-BONELT-HDMI,BB-BONELT-HDMIN,BB-BONE-EMMC-2Gconsole=ttyO0,115200n8mmcroot=/dev/mmcblk0p2
 
rommcrootfstype=ext4 rootwait fixrtcloadkernel=load mmc 
${mmcdev}:${mmcpart} 0x80300000 ${kernel_file}loadinitrd=load mmc 
${mmcdev}:${mmcpart} 0x81600000 ${initrd_file}; setenv initrd_size 
${filesize}loadfdt=load mmc ${mmcdev}:${mmcpart} 0x815f0000 
/dtbs/${fdtfile}boot_ftd=run loadkernel; run loadinitrd; run 
loadfdtdevice_args=run expansion_args; run mmcargsmmcargs=setenv bootargs 
console=${console} ${optargs} ${kms_force_mode} root=${mmcroot} 
rootfstype=${mmcrootfstype} ${expansion} ${systemd}expansion_args=setenv 
expansion ip=${ip_method}uenvcmd=run boot_ftd; run device_args; bootz 
0x80300000 0x81600000:${initrd_size} 0x815f0000#Next line added to preserve 
pwm at bootupoptargs=quiet drm.debug=7 
capemgr.enable_partno=am33xx_pwm,bone_pwm_P9_21#Next line added to preserve 
UART1 (ttyO1) at boot timeoptargs=quiet drm.debug=7 
capemgr.enable_partno=BB-UART1#Disable HDMI 
onlyoptargs=capemgr.disable_partno=BB-BONELT-HDMI,BB-BONELT-HDMIN*


But this is what I get on boot:

root@debian:~# cat /sys/devices/bone_capemgr.*/slots
 0: 54:PF---
 1: 55:PF---
 2: 56:PF---
 3: 57:PF---
 4: ff:P-O-L Bone-LT-eMMC-2G,00A0,Texas Instrument,BB-BONE-EMMC-2G
 5: ff:P-O-- Bone-Black-HDMI,00A0,Texas Instrument,BB-BONELT-HDMI
 6: ff:P-O-- Bone-Black-HDMIN,00A0,Texas Instrument,BB-BONELT-HDMIN

There's no pwm, no uart and ole HDMI's still there. Can anyone explain 
that? Does the uEnv.txt file require things in a special order?

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