IIRC the history of flashing tools basically (2018 to present):

* in the before times, we basically used gdb + openocd or jlinkgdb or similar existing tools
* then `probe-rs` (the library) got written, and `cargo embed` was the main "program" for that, which handled logs and flashing and stuff, lots of configurable options. There was also `cargo flash` that JUST did flashing, not sure which came first
* then `probe-run` (the program, by Ferrous and not the probe-rs developers) came out, had much fewer options than cargo-embed, but did one thing (flash and attach to RTT+defmt logs basically)
* then `probe-rs-cli` came out, which later got renamed to just `probe-rs`, which was kinda in the middle of `probe-run` and `cargo embed` in terms of features
* then since `probe-rs` (the tool) was in active development, and `probe-run` was in maintenance, `probe-run` got deprecated

TL;DR today: `probe-rs run` is probably the best place to start, `probe-rs ...` is what most people use for everything, and `cargo embed` still does a couple things that `probe-rs` doesn't.

If you see old guides/tutorials that recommend `probe-run`, `cargo flash`, maaaaybe `cargo embed`, it'd probably be good to share here in case we can get them updated for modern tooling

(anyone else, please correct me if I'm wrong, this is all from memory)