Migrate to a new PWD API (#12603)

This is the first PR towards migrating to a new `$env.PWD` API that
returns potentially un-canonicalized paths. Refer to PR #12515 for
motivations.

## New API: `EngineState::cwd()`

The goal of the new API is to cover both parse-time and runtime use
case, and avoid unintentional misuse. It takes an `Option<Stack>` as
argument, which if supplied, will search for `$env.PWD` on the stack in
additional to the engine state. I think with this design, there's less
confusion over parse-time and runtime environments. If you have access
to a stack, just supply it; otherwise supply `None`.

## Deprecation of other PWD-related APIs

Other APIs are re-implemented using `EngineState::cwd()` and properly
documented. They're marked deprecated, but their behavior is unchanged.
Unused APIs are deleted, and code that accesses `$env.PWD` directly
without using an API is rewritten.

Deprecated APIs:

* `EngineState::current_work_dir()`
* `StateWorkingSet::get_cwd()`
* `env::current_dir()`
* `env::current_dir_str()`
* `env::current_dir_const()`
* `env::current_dir_str_const()`

Other changes:

* `EngineState::get_cwd()` (deleted)
* `StateWorkingSet::list_env()` (deleted)
* `repl::do_run_cmd()` (rewritten with `env::current_dir_str()`)

## `cd` and `pwd` now use logical paths by default

This pulls the changes from PR #12515. It's currently somewhat broken
because using non-canonicalized paths exposed a bug in our path
normalization logic (Issue #12602). Once that is fixed, this should
work.

## Future plans

This PR needs some tests. Which test helpers should I use, and where
should I put those tests?

I noticed that unquoted paths are expanded within `eval_filepath()` and
`eval_directory()` before they even reach the `cd` command. This means
every paths is expanded twice. Is this intended?

Once this PR lands, the plan is to review all usages of the deprecated
APIs and migrate them to `EngineState::cwd()`. In the meantime, these
usages are annotated with `#[allow(deprecated)]` to avoid breaking CI.

---------

Co-authored-by: Jakub Žádník <kubouch@gmail.com>

crates/nu-command/src/system/exec.rs

@@ -1,4 +1,5 @@
 use super::run_external::create_external_command;
+#[allow(deprecated)]
 use nu_engine::{command_prelude::*, current_dir};
 use nu_protocol::OutDest;
 
@@ -62,6 +63,7 @@ fn exec(
     external_command.out = OutDest::Inherit;
     external_command.err = OutDest::Inherit;
 
+    #[allow(deprecated)]
     let cwd = current_dir(engine_state, stack)?;
     let mut command = external_command.spawn_simple_command(&cwd.to_string_lossy())?;
     command.current_dir(cwd);

crates/nu-command/src/system/which_.rs

@@ -229,6 +229,7 @@ fn which(
 
     let mut output = vec![];
 
+    #[allow(deprecated)]
     let cwd = env::current_dir_str(engine_state, stack)?;
     let paths = env::path_str(engine_state, stack, call.head)?;