diff --git a/AGENTS.md b/AGENTS.md
index 8f561ae..406f6fc 100644
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -17,7 +17,7 @@ public/            ← build output (generated)
 | File | Responsibility |
 |---|---|
 | `main.odin` | Entry point. Sets `context.logger`, calls `init_site`, `walk_content`, `render_site`. Optional Spall profiling via `SPALL` config flag. |
-| `site.odin` | `Flags` (parsed config), `Site` (runtime state + arena), `Feature` bit_set enum, `init_site`, `load_site_config`, `merge_flags`, `site_apply_flags`, `find_config` (walks up dir tree for `thor.json`) |
+| `site.odin` | `Flags` (CLI args), `Config_File` (from `thor.json`), `Site` (runtime state + arena), `Feature` + `Markdown_Extension` bit_set enums, `DEFAULT_MARKDOWN_EXTENSIONS`, 5-step `init_site` (defaults → flags → config → apply config → apply flags), `load_config_file`, `apply_config`, `apply_cli_flags`, `parse_extension_list`, `find_config` |
 | `frontmatter.odin` | JSON frontmatter parser (`{ }` delimited) |
 | `content.odin` | `Page` struct, content walker, page loader, cmark integration, full markdown pipeline, `copy_assets_dir` (recursive copy with CSS minification) |
 | `footnotes.odin` | Note definition stripping (pre-cmark) + sidenote/marginnote injection (post-cmark) |
@@ -36,10 +36,16 @@ Icon SVGs live as HTML partials in `layouts/partials/icons/` (home, github, rss,
 ### Data flow
 
 ```
-thor.json → find_config → init_site → Flags → merge_flags → site_apply_flags → Site (config + Dynamic_Arena + features: bit_set)
-                                                                                              ↓
+thor.json → find_config → init_site:
+  1. set defaults (base_url, DEFAULT_MARKDOWN_EXTENSIONS)
+  2. parse CLI flags (Flags struct)
+  3. load config file (Config_File from thor.json)
+  4. apply_config — non-empty config fields override defaults
+  5. apply_cli_flags — flags override config, -ext/-no-ext adjust extensions
+→ Site (config + Dynamic_Arena + features: bit_set + markdown_extensions: bit_set)
+                                                                                               ↓
 content/ → walk_content → []Page (with body_html from pipeline)
-                                                                                              ↓
+                                                                                               ↓
 layouts/*.html → parse() → mustache.Template (parsed once)
                                    ↓
 render_site → mustache.render(Page_Data, partials) → optional minify_html → public/
@@ -47,12 +53,19 @@ render_site → mustache.render(Page_Data, partials) → optional minify_html 
 
 ### Config system
 
-Config is split into `Flags` (parsed from CLI args + JSON) and `Site` (runtime state):
+Config is split into three structs with a clear 5-step initialization flow:
 
-- **`Flags`** — pure parsed config struct. CLI args via `core:flags`, JSON via `json.unmarshal_string`.
-- **`Site`** — runtime state: arena, resolved config values, `features: bit_set[Feature]`.
-- **`Feature` enum** — `Sections`, `Drafts`, `Minify`, `Watch`. Checked with `.Minify in site.features`.
-- **`find_config`** — walks up from CWD looking for `thor.json`. Falls back to `./thor.json`.
+- **`Flags`** — CLI args only. Parsed by `core:flags`. Includes path overrides, build-mode toggles, and `-ext`/`-no-ext` for markdown extension overrides.
+- **`Config_File`** — parsed from `thor.json` via `json.unmarshal_string`. Holds title, paths, `markdown_extensions` (JSON), `params` (JSON).
+- **`Site`** — runtime state: arena, resolved config values, `features: bit_set[Feature]`, `markdown_extensions: bit_set[Markdown_Extension]`.
+
+**`Feature` enum** — build-mode toggles: `Drafts`, `Minify`, `Watch`. Checked with `.Minify in site.features`.
+
+**`Markdown_Extension` enum** — content pipeline toggles: `Emoji`, `Sidenotes`, `Alerts`, `Highlight`, `Sections`. Default is `DEFAULT_MARKDOWN_EXTENSIONS` (currently `.Emoji, .Sidenotes, .Alerts`). Configurable via:
+- `thor.json`: `"markdown_extensions": { "emoji": true, "highlight": false, ... }`
+- CLI: `-ext:highlight,sections` (enable) / `-no-ext:emoji` (disable). Comma-separated, case-insensitive.
+
+**`find_config`** — walks up from CWD looking for `thor.json`. Falls back to `./thor.json`.
 
 Config precedence: `CLI flags > thor.json values > hardcoded defaults`.
 
@@ -61,7 +74,13 @@ Config precedence: `CLI flags > thor.json values > hardcoded defaults`.
   "title": "...",
   "base_url": "...",
   "author": "...",
-  "sectionate": true,
+  "markdown_extensions": {
+    "emoji": true,
+    "sidenotes": true,
+    "alerts": true,
+    "highlight": true,
+    "sections": true
+  },
   "params": {
     "social": [
       { "name": "github", "url": "...", "icon": "icons/github" }
@@ -86,7 +105,7 @@ Templates use Mustache with template inheritance (`{{<base}}` / `{{$block}}`):
 {{/base}}
 ```
 
-Data is passed as **typed structs** (not `map[string]any`). Mustache resolves struct fields via Odin reflection, including `using`-embedded fields:
+Data is passed as **typed structs** (not `map[string]any`). Mustache resolves struct fields via Odin reflection, including `using`-embedded fields. Date presence is checked via string truthiness (`{{#date_iso}}`) — no separate `has_date` bool needed.
 
 ```odin
 Base_Data :: struct {
@@ -108,16 +127,16 @@ Page_Data :: struct {
 
 ```
 raw markdown
-  → strip_definitions     (pre-cmark: extract [^id]: definitions)
+  → strip_definitions     (pre-cmark: extract [^id]: definitions — only if .Sidenotes enabled)
   → cmark markdown_to_html (Unsafe mode for HTML passthrough)
-  → expand_emoji          (post-cmark: :shortcode: → unicode, avoids cmark escape issues)
-  → inject_notes          (post-cmark: [^id] → <label><input><span> markup)
-  → inject_alerts         (post-cmark: [!TYPE] blockquotes → styled alerts)
-  → highlight_code        (post-cmark: tree-sitter per code block, with error reporting)
-  → wrap_sections         (post-cmark: if .Sections in features, wraps content in <section> at <h2>)
+  → expand_emoji          (post-cmark: :shortcode: → unicode — only if .Emoji enabled)
+  → inject_notes          (post-cmark: [^id] → <label><input><span> markup — only if .Sidenotes enabled)
+  → inject_alerts         (post-cmark: [!TYPE] blockquotes → styled alerts — only if .Alerts enabled)
+  → highlight_code        (post-cmark: tree-sitter per code block — only if .Highlight enabled)
+  → wrap_sections         (post-cmark: wraps content in <section> at <h2> — only if .Sections enabled)
 ```
 
-`.html` content files skip cmark entirely — body is used as-is.
+Each step is gated by `bit_set[Markdown_Extension]`. All `.html` content files skip the pipeline entirely — body is used as-is.
 
 ### Syntax highlighting
 
diff --git a/site.odin b/site.odin
index 0b35ff7..d999081 100644
--- a/site.odin
+++ b/site.odin
@@ -152,7 +152,7 @@ site_apply_config :: proc(site: ^Site, config: Config_File, config_dir: string)
 	site.layouts_dir =
 		config.layouts_dir if config.layouts_dir != "" else fmt.tprintf("%s/layouts", config_dir)
 
-	if params, ok := config.markdown_extensions.(json.Object); ok {
+	if params, ok := config.params.(json.Object); ok {
 		site.params = params
 	}