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-parser/src/parse_keywords.rs

@@ -1949,6 +1949,7 @@ pub fn parse_module_file_or_dir(
         return None;
     }
 
+    #[allow(deprecated)]
     let cwd = working_set.get_cwd();
 
     let module_path =
@@ -3359,6 +3360,7 @@ pub fn parse_source(working_set: &mut StateWorkingSet, lite_command: &LiteComman
         let scoped = name == b"source-env";
 
         if let Some(decl_id) = working_set.find_decl(name) {
+            #[allow(deprecated)]
             let cwd = working_set.get_cwd();
 
             // Is this the right call to be using here?
@@ -3564,6 +3566,7 @@ pub fn parse_register(working_set: &mut StateWorkingSet, lite_command: &LiteComm
 
     let spans = &lite_command.parts;
 
+    #[allow(deprecated)]
     let cwd = working_set.get_cwd();
 
     // Checking that the function is used with the correct name
@@ -3785,6 +3788,7 @@ pub fn parse_register(working_set: &mut StateWorkingSet, lite_command: &LiteComm
 pub fn parse_plugin_use(working_set: &mut StateWorkingSet, call: Box<Call>) -> Pipeline {
     use nu_protocol::{FromValue, PluginRegistryFile};
 
+    #[allow(deprecated)]
     let cwd = working_set.get_cwd();
 
     if let Err(err) = (|| {