Electronic – use a Dupont cable with a resistor soldered in the middle as a pullup resistor for I2C comms

I've recently rolled my own as far as I2C connectors go. The connector itself is not very important, right now I'm just using 100mil pitch header (usually female on board so it's not so pokey when not connected), but any 4plus pin connector will do. Additionally, I'm using the P82B715 from TI as an I2C bus extender. This overcomes the capacitance issues associated with running long I2C drops off board, which as people have been saying, I2C was not intended for initially. I did try many different combinations, like in the examples you gave and I noticed absolutely no difference in performance. I believe this is because I2C is relatively slow, interference between SDA and SCL is not much of an issue. Basically the rise time for voltages (when interference will occur) on the bus are much much smaller than a bit length. So, that may not be what you want to hear, but it does afford more options. Personally I went with [VCC, SDA, GND, SCL] to be easily routed to/from this chip and also be immune to a VCC/GND mix up when plugged in backward.

Seems like just a line omission from the datasheet. On the Pin Description section of Page 6

Pin 5- SDA:

Serial Data Input/Output. SDA is the data input/output for the I2C serial interface. The SDA pin is open drain and requires an external pullup resistor. The pullup voltage can be up to 5.5V regardless of the voltage on VCC.

Pin 6- SCL:

Serial Clock Input. SCL is the clock input for the I2C interface and is used to synchronize data movement on the serial interface. The pullup voltage can be up to 5.5V regardless of the voltage on VCC.

It seems to just skip a line stating that the pin is open drain and requires the external pull up, but then adds the same line afterwards, stating the pull up value. Looking at older versions of the datasheet, back when Maxim Integrated was Maxim-Dallas and even just Dallas Semi, the omission has always been there.

That said, the typical wiring diagram has always been correct, showing the pull up needed on both i2c lines, as the i2c standard requires.

As for the SQW/Out pin, the Pull Up is only required if you are using the line. It can be disabled in the rtc's settings (Or should I say, comes disabled, needs to be turned on). Having a pull up resistor on the line, when you are not going to use it, will waste energy, needlessly draining a battery (Slowly) in battery applications. As the datasheet says, this can be left floating, i.e. no pull up, if not needed. The Adafruit device breaks it out for your convenience if you do want to use it, but you need to add the pull up externally if you want to (or use the Arduino's internal pull-up option)