COMP: Modernize .ruff.toml settings based on ruff v0.3.3

Fixes the following warnings:

```
warning: The top-level linter settings are deprecated in favour of their counterparts in the `lint` section. Please update the following options in `.ruff.toml`:
  - 'per-file-ignores' -> 'lint.per-file-ignores'
warning: `PGH001` has been remapped to `S307`.
warning: `PGH002` has been remapped to `G010`.
```

Since the "S" rules are disabled, simply remove the reference to `PGH001`
instead of adding an exception for `S307`.

.ruff.toml

@@ -66,14 +66,12 @@ extend-ignore = [
   "F841",    # Local variable is assigned to but never used
 
   "G002",    # Logging statement uses `%`
+  "G010",    # `warn` is deprecated in favor of `warning`
 
   "ICN001",  # `numpy` should be imported as `np`
   "ISC002",  # Implicitly concatenated string literals over multiple lines
   "ISC003",  # Explicitly concatenated string should be implicitly concatenated
 
-  "PGH001",  # No builtin `eval()` allowed
-  "PGH002",  # `warn` is deprecated in favor of `warning`
-
   "PLR0912", # Too many branche
   "PLR0913", # Too many arguments in function definition
   "PLR0911", # Too many return statements
@@ -119,7 +117,7 @@ extend-ignore = [
 [lint.pydocstyle]
 convention = "pep257"
 
-[per-file-ignores]
+[lint.per-file-ignores]
 # Module imported but unused
 "Base/Python/mrml.py" = ["F401"]
 "Base/Python/slicer/logic.py" = ["F401"]