Add deprecation warning for ruff-lsp specific settings

package.json

@@ -120,6 +120,8 @@
         "ruff.lint.args": {
           "default": [],
           "markdownDescription": "Additional command-line arguments to pass to `ruff check`, e.g., `\"args\": [\"--config=/path/to/pyproject.toml\"]`. Supports a subset of Ruff's command-line arguments, ignoring those that are required to operate the LSP, like `--force-exclude` and `--verbose`.\n\n**This setting is not supported by the native server.**",
+          "markdownDeprecationMessage": "**Deprecated**: This setting is only used by [`ruff-lsp`](https://github.com/astral-sh/ruff-lsp) which is deprecated in favor of the native language server. Refer to the [migration guide](https://docs.astral.sh/ruff/editors/migration) for more information.",
+          "deprecationMessage": "Deprecated: This setting is only used by ruff-lsp which is deprecated in favor of the native language server.",
           "items": {
             "type": "string"
           },
@@ -194,6 +196,8 @@
             "Run Ruff on every keystroke.",
             "Run Ruff on save."
           ],
+          "markdownDeprecationMessage": "**Deprecated**: This setting is only used by [`ruff-lsp`](https://github.com/astral-sh/ruff-lsp) which is deprecated in favor of the native language server. This setting is irrelevant when using the native language server which runs on every keystroke by default.",
+          "deprecationMessage": "Deprecated: This setting is only used by ruff-lsp which is deprecated in favor of the native language server. This setting is irrelevant when using the native language server which runs on every keystroke by default.",
           "scope": "window",
           "type": "string"
         },
@@ -206,6 +210,8 @@
         "ruff.format.args": {
           "default": [],
           "markdownDescription": "Additional command-line arguments to pass to `ruff format`, e.g., `\"args\": [\"--config=/path/to/pyproject.toml\"]`. Supports a subset of Ruff's command-line arguments, ignoring those that are required to operate the LSP, like `--force-exclude` and `--verbose`.\n\n**This setting is not supported by the native server.**",
+          "markdownDeprecationMessage": "**Deprecated**: This setting is only used by [`ruff-lsp`](https://github.com/astral-sh/ruff-lsp) which is deprecated in favor of the native language server. Refer to the [migration guide](https://docs.astral.sh/ruff/editors/migration) for more information.",
+          "deprecationMessage": "Deprecated: This setting is only used by ruff-lsp which is deprecated in favor of the native language server.",
           "items": {
             "type": "string"
           },
@@ -309,6 +315,8 @@
         "ruff.ignoreStandardLibrary": {
           "default": true,
           "markdownDescription": "Whether to ignore files that are inferred to be part of the Python standard library.",
+          "markdownDeprecationMessage": "**Deprecated**: This setting is only used by [`ruff-lsp`](https://github.com/astral-sh/ruff-lsp) which is deprecated in favor of the native language server. Refer to the [migration guide](https://docs.astral.sh/ruff/editors/migration) for more information.",
+          "deprecationMessage": "Deprecated: This setting is only used by ruff-lsp which is deprecated in favor of the native language server.",
           "scope": "window",
           "type": "boolean"
         },
@@ -344,6 +352,8 @@
         "ruff.showNotifications": {
           "default": "off",
           "markdownDescription": "Controls when notifications are shown by this extension.",
+          "markdownDeprecationMessage": "**Deprecated**: This setting is only used by [`ruff-lsp`](https://github.com/astral-sh/ruff-lsp) which is deprecated in favor of the native language server. Refer to the [migration guide](https://docs.astral.sh/ruff/editors/migration) for more information.",
+          "deprecationMessage": "Deprecated: This setting is only used by ruff-lsp which is deprecated in favor of the native language server.",
           "enum": [
             "off",
             "onError",