docs(extensions): clarify agent-context README and add config examples (#3389)

* docs(extensions): clarify agent-context README and add config examples

Rewrite the agent-context extension README to read as plain prose
instead of a bullet dump, and add the missing install/disable
commands (specify extension add/disable/enable agent-context).
Add inline example comments to agent-context-config.yml for
context_file/context_files.

* docs(agent-context): clarify config documentation

- Reformat comments to flow as single-line paragraphs instead of multi-line breaks
- Add "WHAT" sections describing each configuration option's purpose
- Add "REQUIREMENT" sections specifying if options are optional or required
- Add explicit EXAMPLE sections for context_markers configuration
- Improve clarity of context_file and context_files option descriptions

* docs(agent-context): fix GitHub casing, clarify config

- Fix "Github" -> "GitHub" casing in README issues link
- Clarify agent-context-config.yml comments on context_file/context_files behavior and precedence

* YAML indentation fix for context markers

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

* docs(agent-context): simplify README config section

- Clarify config file path reference (.specify/extensions path vs repo path)
- Remove duplicated YAML example/field docs from README, point to config file directly
- Minor spacing fix in agent-context-config.yml comment

* docs(agent-context): clarify config file path in README

- Reference the installed .specify config path alongside the repo-relative link

* docs(agent-context): clarify install and marker requirement

- README: clarify install command must be run from an initialized Spec Kit project root
- config: correct context_markers requirement from REQUIRED to OPTIONAL

* Wording Fix

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

* docs(agent-context): clarify context_file path rules

- Document that context_file/context_files are relative to the project root (directory containing .specify/)
- State the rejected path forms (absolute paths, backslash separators, .. segments) directly in each field's WHAT comment

* Updated supported invocation syntaxes

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

* Extension Disable Clarification

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

* docs(agent-context): document .mdc frontmatter exception

- Clarify that .mdc files get alwaysApply: true set in frontmatter, outside the managed marker block
- Fix "Everything else is untouched" wording so it doesn't contradict the exception right above it

---------

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

Author: yanukadeneth99

extensions/agent-context/README.md

@@ -2,66 +2,62 @@
 
 This bundled extension manages the **coding agent context/instruction file** (e.g. `CLAUDE.md`, `.github/copilot-instructions.md`, `AGENTS.md`, `GEMINI.md`, …) for the active integration.
 
-It owns the lifecycle of the managed section delimited by the configurable start/end markers (defaults: `<!-- SPECKIT START -->` / `<!-- SPECKIT END -->`).
+It owns the lifecycle of the managed section delimited by the configurable start/end markers (defaults: `<!-- SPECKIT START -->` / `<!-- SPECKIT END -->`). For `.mdc` files, it also ensures the YAML frontmatter (the metadata block at the top of the file) contains `alwaysApply: true`. Otherwise, everything outside the managed section is untouched.
+
+> NOTE: Spec Kit itself never touches your agent context file. This extension is the only thing that does, and it's opt-in: install it if you want the block kept in sync, skip it if you'd rather manage that file yourself.
 
 ## Why an extension?
 
 Not every Spec Kit user wants Spec Kit to write into the coding agent's context file. Keeping this behavior in a dedicated, **opt-in** extension lets users:
 
-- **Choose whether to install it at all** — `specify init` does not install it. Add it explicitly when you want Spec Kit to manage the agent context file; if it is absent or disabled, Spec Kit never creates or modifies that file.
-- **Customize the markers** by editing `.specify/extensions/agent-context/agent-context-config.yml` — the bundled scripts honor the `context_markers` value.
+- **Choose whether to install it at all** - `specify init` does **not** install it. Add it explicitly when you want Spec Kit to manage the agent context file; when it is absent, the file is never modified, and when it is disabled, its automatic hooks do not run.
+- **Customize the markers** by editing `.specify/extensions/agent-context/agent-context-config.yml` ([agent-context-config.yml](./agent-context-config.yml) in this repo) - the bundled scripts honor the `context_markers` value.
 - **Synchronize multiple agent anchors** by setting `context_files` when a project intentionally uses more than one coding agent context file, such as `AGENTS.md` and `CLAUDE.md`.
-- **Refresh on demand** by running the `speckit.agent-context.update` command in your agent, or automatically through the hooks declared in `extension.yml` (`after_specify`, `after_plan`). Invoke it using your agent's slash-command separator — `/speckit.agent-context.update` for dot-separator agents or `/speckit-agent-context-update` for hyphen-separator agents (e.g. Forge, Cline).
+- **Refresh on demand** by running the `speckit.agent-context.update` command in your agent, or automatically through the hooks declared in [extension.yml](./extension.yml) (`after_specify`, `after_plan`).
 
-## Commands
+## Installation
 
-The command ID below is canonical. When invoking it as a slash command, use your agent's separator: `/speckit.agent-context.update` for dot-separator agents or `/speckit-agent-context-update` for hyphen-separator agents (e.g. Forge, Cline).
+To install the extension, from the root of an initialized Spec Kit project, run:
 
-| Command | Description |
-|---------|-------------|
-| `speckit.agent-context.update` | Refresh the managed section in the agent context file with the current plan path. |
+```bash
+specify extension add agent-context
+```
 
-## Configuration
+## Disabling
 
-All configuration flows through the extension's own config file at
-`.specify/extensions/agent-context/agent-context-config.yml`:
+```bash
+specify extension disable agent-context
 
-```yaml
-# Path to the coding agent context file managed by this extension
-context_file: CLAUDE.md
+# Re-enable it
+specify extension enable agent-context
+```
 
-# Optional list of coding agent context files to manage together.
-# When non-empty, this takes precedence over context_file.
-context_files:
-  - AGENTS.md
-  - CLAUDE.md
+While this extension is disabled (or not installed), nothing in Spec Kit creates, updates, or removes the managed block - the `__CONTEXT_FILE__` placeholder in any template is left as-is, and the extension's own config is never read.
 
-# Delimiters for the managed Spec Kit section
-context_markers:
-  start: "<!-- SPECKIT START -->"
-  end: "<!-- SPECKIT END -->"
-```
+## Commands
+
+| Command                        | Description                                                                       |
+| ------------------------------ | --------------------------------------------------------------------------------- |
+| `speckit.agent-context.update` | Refresh the managed section in the agent context file with the current plan path. |
+
+> NOTE: The command ID above is canonical. Invoke it using the syntax for your integration: `/speckit.agent-context.update` for dot-command integrations; `/speckit-agent-context-update` for hyphen/skills integrations (including Forge and Cline); `$speckit-agent-context-update` for Codex or ZCode in skills mode; or `/skill:speckit-agent-context-update` for Kimi.
+
+## Configuration
 
-- `context_file` — the project-relative path to the coding agent context file. When empty, the bundled update scripts self-seed it by looking up the active integration's key in this extension's own `agent-context-defaults.json` map. The Specify CLI is never consulted.
-- `context_files` — optional project-relative paths to multiple coding agent context files. When non-empty, the list takes precedence over `context_file`. Absolute paths, backslash separators, and `..` path segments are rejected.
-- `context_markers.start` / `.end` — the delimiters around the managed section. Edit these to use custom markers.
+All configuration flows through the extension's own config file at `.specify/extensions/agent-context/agent-context-config.yml` ([agent-context-config.yml](./agent-context-config.yml) in the repo).
 
 ## Requirements
 
 The bundled update scripts require **Python 3** with **PyYAML** for YAML/upsert processing (PowerShell can also use `ConvertFrom-Yaml` when available).
 
-PyYAML ships with the `specify` CLI and is normally available via the same `python3` interpreter. If a hook reports *"PyYAML is required … not available in the current Python environment"*, it means the system `python3` differs from the one used to install Spec Kit. To resolve, run:
+PyYAML ships with the `specify` CLI and is normally available via the same `python3` interpreter. If a hook reports _"PyYAML is required … not available in the current Python environment"_, it means the system `python3` differs from the one used to install Spec Kit. To resolve, run:
 
 ```bash
 pip install pyyaml
 # or target the specific interpreter Spec Kit uses:
 /path/to/speckit-python -m pip install pyyaml
 ```
 
-## Disable
-
-```bash
-specify extension disable agent-context
-```
+## Issues
 
-When disabled (or never installed), Spec Kit performs no agent context file creation, updates, or removal — the extension's bundled scripts are the only code that ever touches the managed section. The Specify CLI carries no agent-context state at all: it never reads this config, never resolves a context file, and the `__CONTEXT_FILE__` placeholder (if present in any template) is left untouched. All context-file knowledge — including the per-agent default mapping in `agent-context-defaults.json` — lives entirely within this extension, so disabling it is a complete opt-out.
+For any other issues, please create an issue in the [official GitHub repo](https://github.com/github/spec-kit/issues).

extensions/agent-context/agent-context-config.yml

@@ -1,20 +1,24 @@
 # Coding Agent Context Extension Configuration
-# These values are populated automatically by `specify init` and
-# `specify integration use` / `specify integration install`.
 
-# Path (relative to the project root) to the default coding agent context file
-# managed by this extension (e.g. CLAUDE.md, AGENTS.md,
-# .github/copilot-instructions.md). Set automatically from the active
-# integration and regenerated during `specify init` or integration switches.
+# WHAT: The single agent context file relative to the project root (the directory containing .specify/). Absolute paths, backslash separators, and `..` path segments are rejected.
+# REQUIREMENT: OPTIONAL. Use this if you want to manually specify a single context file. If you leave this entry blank, it will use the default context file for the coding agent you picked when you set up Spec Kit. See `agent-context-defaults.json` for the defaults.
+# EXAMPLE: context_file: CLAUDE.md
 context_file: ""
 
-# Optional list of project-relative coding agent context files managed by this
-# extension. When non-empty, this list takes precedence over `context_file`.
-# Use this for projects that intentionally keep multiple agent anchors in sync.
+# WHAT: List of agent context files relative to the project root (the directory containing .specify/). If you have both `context_file` and `context_files` filled, then this (`context_files`) takes precedence. Absolute paths, backslash separators, and `..` path segments are rejected.
+# REQUIREMENT: OPTIONAL. Use this if your project requires you to keep multiple agent context files in sync.
+# EXAMPLE:
+# context_files:
+#   - AGENTS.md
+#   - CLAUDE.md
 context_files: []
 
-# Delimiters for the managed Spec Kit section.
-# Edit these to use custom markers.
+# WHAT: Markers (delimiters) for the managed Spec Kit section. This extension injects information only between these markers.
+# REQUIREMENT: OPTIONAL. Only change if you wish to have a custom marker name.
+# EXAMPLE:
+# context_markers:
+#   start: "<!-- AGENT SPEC KIT CONTEXT START -->"
+#   end: "<!-- AGENT SPEC KIT CONTEXT END -->"
 context_markers:
   start: "<!-- SPECKIT START -->"
   end: "<!-- SPECKIT END -->"