diff --git a/schema/mise.json b/schema/mise.json
index a3ca55dd2f..4a02f30ee3 100644
--- a/schema/mise.json
+++ b/schema/mise.json
@@ -1,6 +1,6 @@
 {
   "$id": "https://mise.jdx.dev/schema/mise.json",
-  "$schema": "http://json-schema.org/draft-07/schema#",
+  "$schema": "http://json-schema.org/2019-09/schema#",
   "title": "mise",
   "type": "object",
   "$defs": {
@@ -148,12 +148,13 @@
         },
         "asdf": {
           "description": "use asdf as a default plugin backend",
-          "deprecated": "Use disable_backends instead.",
-          "type": "boolean"
+          "type": "boolean",
+          "deprecated": true
         },
         "asdf_compat": {
           "description": "set to true to ensure .tool-versions will be compatible with asdf",
-          "type": "boolean"
+          "type": "boolean",
+          "deprecated": true
         },
         "cache_prune_age": {
           "default": "30d",
@@ -172,7 +173,8 @@
         },
         "cargo_binstall": {
           "description": "Use cargo-binstall instead of cargo install if available",
-          "type": "boolean"
+          "type": "boolean",
+          "deprecated": true
         },
         "cd": {
           "description": "Path to change to after launching mise",
@@ -215,8 +217,8 @@
         },
         "disable_default_shorthands": {
           "description": "Disables built-in shorthands to asdf/vfox plugins",
-          "deprecated": "Replaced with `disable_default_registry`",
-          "type": "boolean"
+          "type": "boolean",
+          "deprecated": true
         },
         "disable_hints": {
           "default": [],
@@ -243,7 +245,7 @@
           }
         },
         "env_file": {
-          "description": "Path to a file containing environment variables.",
+          "description": "Path to a file containing environment variables to automatically load.",
           "type": "string"
         },
         "erlang": {
@@ -299,8 +301,8 @@
         },
         "go_set_gopath": {
           "description": "[deprecated] Set to true to set GOPATH=~/.local/share/mise/installs/go/.../packages.",
-          "deprecated": "Use env._go.set_goroot instead.",
-          "type": "boolean"
+          "type": "boolean",
+          "deprecated": true
         },
         "go_set_goroot": {
           "default": true,
@@ -345,14 +347,14 @@
         "legacy_version_file": {
           "default": true,
           "description": "Set to false to disable the idiomatic version files such as .node-version, .ruby-version, etc.",
-          "deprecated": "Use idiomatic_version_file instead.",
-          "type": "boolean"
+          "type": "boolean",
+          "deprecated": true
         },
         "legacy_version_file_disable_tools": {
           "default": [],
           "description": "Specific tools to disable idiomatic version files for.",
-          "deprecated": "Use idiomatic_version_file_disable_tools instead.",
           "type": "array",
+          "deprecated": true,
           "items": {
             "type": "string"
           }
@@ -452,7 +454,8 @@
         },
         "profile": {
           "description": "Profile to use for mise.${MISE_PROFILE}.toml files.",
-          "type": "string"
+          "type": "string",
+          "deprecated": true
         },
         "python": {
           "additionalProperties": false,
@@ -492,8 +495,8 @@
             },
             "venv_auto_create": {
               "description": "Automatically create virtualenvs for python tools.",
-              "deprecated": "Use env._python.venv instead.",
-              "type": "boolean"
+              "type": "boolean",
+              "deprecated": true
             },
             "venv_stdlib": {
               "description": "Prefer to use venv from Python's standard library.",
@@ -503,48 +506,48 @@
         },
         "python_compile": {
           "description": "If true, compile python from source. If false, use precompiled binaries. If not set, use precompiled binaries if available.",
-          "deprecated": "Use python.compile instead.",
-          "type": "boolean"
+          "type": "boolean",
+          "deprecated": true
         },
         "python_default_packages_file": {
           "description": "Path to a file containing default python packages to install when installing python.",
-          "deprecated": "Use python.default_packages_file instead.",
-          "type": "string"
+          "type": "string",
+          "deprecated": true
         },
         "python_patch_url": {
           "description": "URL to fetch python patches from.",
-          "deprecated": "Use python.patch_url instead.",
-          "type": "string"
+          "type": "string",
+          "deprecated": true
         },
         "python_patches_directory": {
           "description": "Directory to fetch python patches from.",
-          "deprecated": "Use python.patch_url instead.",
-          "type": "string"
+          "type": "string",
+          "deprecated": true
         },
         "python_precompiled_arch": {
           "description": "Specify the architecture to use for precompiled binaries.",
-          "deprecated": "Use python.precompiled_arch instead.",
-          "type": "string"
+          "type": "string",
+          "deprecated": true
         },
         "python_precompiled_os": {
           "description": "Specify the OS to use for precompiled binaries.",
-          "deprecated": "Use python.precompiled_os instead.",
-          "type": "string"
+          "type": "string",
+          "deprecated": true
         },
         "python_pyenv_repo": {
           "description": "URL to fetch pyenv from for compiling python.",
-          "deprecated": "Use python.pyenv_repo instead.",
-          "type": "string"
+          "type": "string",
+          "deprecated": true
         },
         "python_venv_auto_create": {
           "description": "Automatically create virtualenvs for python tools.",
-          "deprecated": "Use env._python.venv instead.",
-          "type": "boolean"
+          "type": "boolean",
+          "deprecated": true
         },
         "python_venv_stdlib": {
           "description": "Prefer to use venv from Python's standard library.",
-          "deprecated": "Use python.venv_stdlib instead.",
-          "type": "boolean"
+          "type": "boolean",
+          "deprecated": true
         },
         "quiet": {
           "description": "Suppress all output except errors.",
@@ -665,7 +668,8 @@
         "task_run_auto_install": {
           "default": true,
           "description": "Automatically install missing tools when executing tasks.",
-          "type": "boolean"
+          "type": "boolean",
+          "deprecated": true
         },
         "task_skip": {
           "default": [],
@@ -717,8 +721,8 @@
         },
         "vfox": {
           "description": "Use vfox as a default plugin backend instead of asdf.",
-          "deprecated": "Use disable_backends instead.",
-          "type": "boolean"
+          "type": "boolean",
+          "deprecated": true
         },
         "windows_default_file_shell_args": {
           "default": "cmd /c",
diff --git a/settings.toml b/settings.toml
index 9e8fed37ad..4a2ce78f84 100644
--- a/settings.toml
+++ b/settings.toml
@@ -97,6 +97,7 @@ default to using an asdf plugin for cmake.
 env = "MISE_ASDF_COMPAT"
 type = "Bool"
 hide = true
+deprecated = "no longer supported"
 description = "set to true to ensure .tool-versions will be compatible with asdf"
 docs = """
 Only output `.tool-versions` files in `mise local|global` which will be usable by asdf.
@@ -139,6 +140,7 @@ mise use -g cargo-binstall
 [cargo_binstall]
 type = "Bool"
 hide = true
+deprecated = "Use cargo.binstall instead."
 optional = true
 description = "Use cargo-binstall instead of cargo install if available"
 
@@ -241,8 +243,7 @@ They will be read in order, with the last one taking precedence.
 env = "MISE_ENV_FILE"
 type = "Path"
 optional = true
-description = "Path to a file containing environment variables."
-hide = true
+description = "Path to a file containing environment variables to automatically load."
 
 [erlang.compile]
 env = "MISE_ERLANG_COMPILE"
@@ -576,6 +577,7 @@ env = "MISE_PROFILE"
 type = "String"
 description = "Profile to use for mise.${MISE_PROFILE}.toml files."
 optional = true
+deprecated = "Use MISE_ENV_FILE instead."
 hide = true
 
 [python.compile]
@@ -882,6 +884,7 @@ env = "MISE_TASK_RUN_AUTO_INSTALL"
 type = "Bool"
 default = true
 hide = true
+deprecated = "Use task_auto_install instead."
 description = "Automatically install missing tools when executing tasks."
 
 [task_skip]
diff --git a/xtasks/render/settings.ts b/xtasks/render/settings.ts
index 9eeb7fa970..cdff398390 100644
--- a/xtasks/render/settings.ts
+++ b/xtasks/render/settings.ts
@@ -6,7 +6,7 @@ import { match } from "ts-pattern";
 type Element = {
   default: string | number | boolean;
   description: string;
-  deprecated: boolean;
+  deprecated?: boolean;
   type: string;
   enum?: string[];
   items?: {
@@ -18,7 +18,7 @@ type Props = {
   type: string;
   default: string | number | boolean;
   description: string;
-  deprecated: boolean;
+  deprecated: string;
   enum?: [string][];
 };
 
@@ -55,10 +55,12 @@ function buildElement(key: string, props: Props): Element {
   const ele: Element = {
     default: props.default,
     description: props.description,
-    deprecated: props.deprecated,
     type,
   };
 
+  if (props.deprecated) {
+    ele.deprecated = true;
+  }
   if (props.enum) {
     ele.enum = props.enum.map((e) => e[0]);
   }
@@ -87,6 +89,9 @@ for (const key in doc) {
         description: props.description,
         properties: {},
       };
+      if (props.deprecated) {
+        settings[key].deprecated = true;
+      }
       settings[key].properties[subkey] = buildElement(
         `${key}.${subkey}`,
         props[subkey],