Running kernel 4.4 and trying to read a DS3234 clock on the second SPI
port I can suppress the HDMI pins in uEnv.txt with:

dtb=am335x-boneblack-emmc-overlay.dtb
optargs=cape_disable=bone_capemgr.disable_partno=BB-BONELT-HDMI,BB-BONELT-HDMIN

(uEnv.txt isn't loading the "universal overlay".)

Loading BB-SPIDEV0 and BB-SPI1CLK then produces the expected /dev/spidev1.0,
/dev/spidev1.1 and /dev/rtc1 devices.

dmesg says:
bone_capemgr bone_capemgr: part_number 'BB-SPI1CLK', version 'N/A'
bone_capemgr bone_capemgr: slot #6: override
bone_capemgr bone_capemgr: Using override eeprom data at slot 6
bone_capemgr bone_capemgr: slot #6: 'Override Board Name,00A0,Override 
Manuf,BB-SPI1CLK'
ds3234 spi2.0: Control Reg: 0x00
ds3234 spi2.0: Ctrl/Stat Reg: 0x00
ds3234 spi2.0: rtc core: registered ds3234 as rtc1
bone_capemgr bone_capemgr: slot #6: dtbo 'BB-SPI1CLK-00A0.dtbo' loaded; 
overlay id #1

However, there's no spi pingroup, and the relevant pins remain in mode 7
not mode 3, and are unclaimed:

pin 100 (44e10990.0) 00000027 pinctrl-single 
pin 101 (44e10994.0) 00000027 pinctrl-single 
pin 102 (44e10998.0) 00000027 pinctrl-single 
pin 103 (44e1099c.0) 00000027 pinctrl-single 

pin 100 (44e10990.0): (MUX UNCLAIMED) (GPIO UNCLAIMED)
pin 101 (44e10994.0): (MUX UNCLAIMED) (GPIO UNCLAIMED)
pin 102 (44e10998.0): (MUX UNCLAIMED) (GPIO UNCLAIMED)
pin 103 (44e1099c.0): (MUX UNCLAIMED) (GPIO UNCLAIMED)

and reading the clocks gives:

quid ~ # hwclock -f /dev/rtc0 -r
Sat Jul  2 21:00:10 2016  .954216 seconds
quid ~ # hwclock -f /dev/rtc1 -r
hwclock: ioctl(RTC_RD_TIME) to /dev/rtc1 to read the time failed: Invalid 
argument
quid ~ # 

The clock overlay worked in 3.8, and I _think_ I've updated it correctly for
4.4.  Can anyone spot what I've missed?

/*
** Dallas DS3234 RTC SPI driver test.
**
** Virtual cape for SPI1 on connector pins P9.29 P9.31 P9.30 P9.28
**
** Pin Identities.
**
** SPI_1 names     : CS0,   DO,    DI,    CLK
** P9 pins         : 28,    29,    30,    31
** GPIO3 pins      : 17,    15,    16,    14
** Processor pins  : C12,   B13,   D12,   A13
** SRM table 15 ?? : 214,   210,   212,   218
** Pingroup labels : 103,   101,   ???    100
** Code offsets    : 0x19c, 0x194, 0x198, 0x190
** Base pin gpmc_ad0 has address 0x800 giving:
**                 : 0x99c, 0x994, 0x998, 0x990
** TRM 9.3 (spi0)  : 0x95c, 0x954, 0x958, 0x950
**
** Moved to kernel 4.x GPIO bank numbering.
*/

/dts-v1/;
/plugin/;

/ {
    compatible = "ti,beaglebone", "ti,beaglebone-black";

    /* identification */
    part-number = "BB-SPI1CLK";
    version = "00A0";

    /* Resources */
    exclusive-use =
        /* Pin header */
        "P9.31",    /* spi1_sclk */
        "P9.29",    /* spi1_d0 */
        "P9.30",    /* spi1_d1 */
        "P9.28",    /* spi1_cs0 */
        /* Hardware */
        "spi1";

    fragment@0 {
        target = <&am33xx_pinmux>;
        __overlay__ {
            /* Default has all gpios released, mode uart1 */
            pinctrl_spi1: pinctrl_spi1_pins {
                pinctrl-single,pins = <
                    0x190 0x33 /* P9_31 = mcasp0_aclkx.spi1_sclk, 
INPUT_PULLUP | MODE3 */
                    0x194 0x33 /* P9_29 = mcasp0_fsx.spi1_d0, INPUT_PULLUP  
| MODE3 */
                    0x198 0x13 /* P9_30 = mcasp0_axr0.spi1_d1, 
OUTPUT_PULLUP | MODE3 */
                    0x19c 0x13 /* P9_28 = mcasp0_ahclkr.spi1_cs0, 
OUTPUT_PULLUP | MODE3 */
                >;
            };
        };
    };

    fragment@1 {
        target = <&spi1>;
        __overlay__ {
            #address-cells = <1>;
            #size-cells = <0>;
            status           = "okay";
            pinctrl-names    = "default";
            pinctrl-0        = <&pinctrl_spi1>;
            cs-gpios = <&gpio3 17 0>;  /* Is this needed ??? */
            ds3234@0 {
                #address-cells = <1>;
                #size-cells = <0>;
                compatible = "ds3234";
                reg = <0>;
                spi-max-frequency = <200000>; /* Slowed for testing */
                /* spi-cpha ??? */
            };
        };
    };

};


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