refactor(cli): apply simplify findings (Plan B Phases 4-6 polish)

- session.rs: drop save_manifest_raw — its only caller was
  after_manifest_change itself; the pub(crate) advertised the exact
  bypass-the-cache-refresh footgun the wrapper exists to eliminate.
  Inline the encrypt + atomic_write pair.
- session.rs: into_kdf_params(self) → to_kdf_params(&self). Body just
  copies three u32s; the consume-self had no ownership benefit and
  forced the round-trip test to rebuild a ParamsFile field-by-field.
- helpers.rs: add git_rm(repo, paths, context) wrapper around git_run
  + the load-bearing --ignore-unmatch flag. Replaces two near-identical
  three-line "build rm_args, extend, git_run" blocks in trash.rs.
- trash.rs: purge_item_filesystem drops the if x.exists() pre-checks
  (TOCTOU + redundant stat per item per trash-empty iteration). Uses
  ErrorKind::NotFound swallow on remove_file/remove_dir_all instead.
- basic_flows.rs: trim trash_empty_batches_into_one_commit's sleep
  comment to just the WHY.

crates/relicario-cli/tests/basic_flows.rs

@@ -135,8 +135,8 @@ fn trash_empty_batches_into_one_commit() {
     let out = v.run(&["settings", "trash-retention", "--days", "0"]);
     assert!(out.status.success(), "settings trash-retention failed");
 
-    // Brief sleep to ensure now > trashed_at by at least 1 second
-    // (otherwise should_purge returns false at strict-greater-than equality).
+    // should_purge uses strict > on (now - trashed_at), so equal-second
+    // timestamps don't qualify.
     std::thread::sleep(std::time::Duration::from_secs(1));
 
     // Count commits before.