Migrate to a new PWD API (part 2) (#12749)

Refer to #12603 for part 1.

We need to be careful when migrating to the new API, because the new API
has slightly different semantics (PWD can contain symlinks). This PR
handles the "obviously safe" part of the migrations. Namely, it handles
two specific use cases:

* Passing PWD into `canonicalize_with()`
* Passing PWD into `EngineState::merge_env()`

The first case is safe because symlinks are canonicalized away. The
second case is safe because `EngineState::merge_env()` only uses PWD to
call `std::env::set_current_dir()`, which shouldn't affact Nushell. The
commit message contains detailed stats on the updated files.

Because these migrations touch a lot of files, I want to keep these PRs
small to avoid merge conflicts.

crates/nu-cmd-base/src/util.rs

@@ -13,8 +13,7 @@ pub fn get_init_cwd() -> PathBuf {
 }
 
 pub fn get_guaranteed_cwd(engine_state: &EngineState, stack: &Stack) -> PathBuf {
-    #[allow(deprecated)]
-    nu_engine::env::current_dir(engine_state, stack).unwrap_or_else(|e| {
+    engine_state.cwd(Some(stack)).unwrap_or_else(|e| {
         let working_set = StateWorkingSet::new(engine_state);
         report_error(&working_set, &e);
         crate::util::get_init_cwd()