I would not want to see this merged, so as to not encourage in-circuit flashing on boards which are not designed for that due to the potential risks involved.
Breaking hardware is easier than one could think: just powering a mainboard via a clip can violate the power sequencing requirements of the board and damage to other ICs on the board. Even using an external power supply could harm some boards. Overloading data pins is very easy to do. Even using an ohmeter (multimeter in resistance mode) on an unpowered board can kill circuits.
Let's see some examples. Let's suppose we have a chip (e.g. a southbridge) that uses two voltage rails: rail A (3.3V) and rail B (1.8V). Suppose we're only powering one rail at a time, while the other rail is left unpowered (therefore, at zero volts). The voltage difference between both rails (A - B) changes significantly:
Normal: 3.3V - 1.8V = 1.5V
Only rail A: 3.3V - 0V = 3.3V
Only rail B: 0V - 1.8V = -1.8V
The rail A case means that some parts of the chip would see more than twice of the voltage they expect. Doesn't look good.
The rail B case is even worse: some parts of the chip would be reverse-biased (powered backwards). I don't even want to think about it.
If there are protection diodes, you could survive such a disaster. But how do you know they are installed in first place? They could be omitted on designs with a strict power sequence, or on cheap designs. Moreover, if any of these diodes is clamping the voltage down to a safe level, this means more current is drawn from the programmer. Most 3.3V regulators on flashers are tiny and easy to overload, and their failure mode usually results in them passing through their input voltage to the output, which is usually 5V from the USB ports. Then, everything gets overvolted, and things die.
Some people suggest using a beefier external power supply, such as an ATX computer PSU, if the flasher is not giving out enough power. That is an insane recommendation nobody should ever follow unless their goal is to light that board on fire. If any clamp circuits were active and overloading the flasher's (relatively weak) voltage source to protect the board, they will now have to handle currents of up to a few dozen amps, coming from the external PSU. Do you like fireworks?
If you're powering the board using its own power supply, so that the flash chip is powered by the board itself, not the programmer, then you have to deal with the other active masters on the SPI bus (ideally, just one). If you can make all of them stay idle or in reset, the SPI bus should be inactive and you should be able to flash without requiring this mode.
If you can't make the other SPI masters shut up, then your flasher will be fighting with the other masters on the SPI bus. Data corruption aside, if a master drives a pin high while the other one drives the same pin low, then we have problems.
If the circuit board has resistors between the flash chip and the onboard masters, the onboard masters will have a higher impedance than your flasher, so theoretically you could probably flash fine without needing this mode.
However, if the board has no resistors between the masters (usually the case on cheap boards), you have a short-circuit. On most SPI masters, the absolute maximum allowable current flowing through I/O pins is very low. A short-circuit can easily kill those pins, and thus render the SPI interface useless. And killing a CH341A that way will hurt much less than killing a computer mainboard with a soldered CPU.
If somebody wants to flash a mainboard which is not designed to be flashed in-circuit, they should consider removing the flash chip. If flashing needs to be done regularly, then they should consider making the flash chip easily removable by installing a socket, or modifying the board so that it can handle in-circuit flashing: a diode on VCC to prevent powering the rest of the board, and resistors on the data signals to avoid driving outputs. Some boards' design makes the last option impossible to sanely implement, though.
I can see why people want to avoid doing any of the above: it involves using soldering equipment on rather small components. Without soldering, there's no good solution.
Patch set 6:
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