feat: make agent-context extension a full opt-in

AGENTS.md

@@ -75,7 +75,6 @@ class WindsurfIntegration(MarkdownIntegration):
         "args": "$ARGUMENTS",
         "extension": ".md",
     }
-    context_file = ".windsurf/rules/specify-rules.md"
 ```
 
 **TOML agent (Gemini):**
@@ -101,7 +100,6 @@ class GeminiIntegration(TomlIntegration):
         "args": "{{args}}",
         "extension": ".toml",
     }
-    context_file = "GEMINI.md"
 ```
 
 **Skills agent (Codex):**
@@ -129,7 +127,6 @@ class CodexIntegration(SkillsIntegration):
         "args": "$ARGUMENTS",
         "extension": "/SKILL.md",
     }
-    context_file = "AGENTS.md"
 
     @classmethod
     def options(cls) -> list[IntegrationOption]:
@@ -150,7 +147,6 @@ class CodexIntegration(SkillsIntegration):
 | `key` | Class attribute | Unique identifier; for CLI-based integrations (`requires_cli: True`), must match the CLI executable name |
 | `config` | Class attribute (dict) | Agent metadata: `name`, `folder`, `commands_subdir`, `install_url`, `requires_cli` |
 | `registrar_config` | Class attribute (dict) | Command output config: `dir`, `format`, `args` placeholder, file `extension` |
-| `context_file` | Class attribute (str or None) | Path to agent context/instructions file (e.g., `"CLAUDE.md"`, `".github/copilot-instructions.md"`) |
 
 **Key design rule:** For CLI-based integrations (`requires_cli: True`), `key` must be the actual executable name (e.g., `"cursor-agent"` not `"cursor"`). This ensures `shutil.which(key)` works for CLI-tool checks without special-case mappings. IDE-based integrations (`requires_cli: False`) should use their canonical identifier (e.g., `"windsurf"`, `"copilot"`).
 
@@ -175,9 +171,11 @@ def _register_builtins() -> None:
 
 ### 4. Context file behavior
 
-Set `context_file` on the integration class. The base integration setup creates or updates the managed Spec Kit section in that file, and uninstall removes the managed section when appropriate.
+The Specify CLI carries **no agent-context state whatsoever**. Integration classes do **not** declare a `context_file`, and the CLI never creates, updates, removes, resolves, or migrates a context/instruction file (`CLAUDE.md`, `AGENTS.md`, `.github/copilot-instructions.md`, …). New integrations add nothing for context handling.
 
-The managed section is owned by the bundled `agent-context` extension (`extensions/agent-context/`). All configuration flows through the extension's own config file at `.specify/extensions/agent-context/agent-context-config.yml`:
+Managing the "Spec Kit" section in the context file is fully owned by the bundled `agent-context` extension (`extensions/agent-context/`), which is a **full opt-in**: `specify init` does not install it. A user adds/enables it through the standard extension verbs, after which the extension's own bundled scripts maintain the context section. When the extension is absent or disabled, nothing in Spec Kit touches the context file.
+
+The extension reads its own config file at `.specify/extensions/agent-context/agent-context-config.yml`:
 
 ```yaml
 # Path to the coding agent context file managed by this extension
@@ -189,10 +187,10 @@ context_markers:
   end: "<!-- SPECKIT END -->"
 ```
 
-- `context_file` is written automatically from the integration's class attribute when `specify init` or `specify integration use` is run.
-- `context_markers.{start,end}` defaults to `IntegrationBase.CONTEXT_MARKER_START` / `CONTEXT_MARKER_END`. Users who want custom markers edit `agent-context-config.yml` directly — both the Python layer (`upsert_context_section()` / `remove_context_section()`) and the bundled scripts (`extensions/agent-context/scripts/bash/update-agent-context.sh` and `.ps1`) read from this single source of truth.
+- The Specify CLI does **not** write this config. When `context_file` is empty, the extension's bundled scripts self-seed it by looking up the active integration's key in the extension's own `agent-context-defaults.json` map (`extensions/agent-context/scripts/bash/update-agent-context.sh` and `.ps1`). The CLI registry is never consulted — all agent→context-file knowledge lives inside the extension.
+- `context_markers.{start,end}` are read solely by the extension's scripts; they default to the Spec Kit markers shown above and can be customized by editing `agent-context-config.yml` directly.
 
-Users can opt out entirely with `specify extension disable agent-context`; while disabled, Spec Kit skips context-file creation, updates, and removal (the gates are inside `upsert_context_section()` and `remove_context_section()`).
+Existing projects created by older Spec Kit versions keep working: any previously written managed section or extension config is left intact and is only ever updated by the extension when run.
 
 Only add custom setup logic when the agent needs non-standard behavior. Integrations no longer require per-agent thin wrapper scripts or shared context-update dispatcher scripts — the `agent-context` extension is fully generic.
 
@@ -401,7 +399,6 @@ Implementation: Extends `YamlIntegration` (parallel to `TomlIntegration`):
 2. Extracts title and description from frontmatter
 3. Renders output as Goose recipe YAML (version, title, description, author, extensions, activities, prompt)
 4. Uses `yaml.safe_dump()` for header fields to ensure proper escaping
-5. Sets `context_file = "AGENTS.md"` so the base setup manages the Spec Kit context section there
 
 ## Branch Naming Convention
 
@@ -466,7 +463,7 @@ Disclosure is **continuous**, not a one-time event. A single AI-disclosure parag
 ## Common Pitfalls
 
 1. **Using shorthand keys for CLI-based integrations**: For CLI-based integrations (`requires_cli: True`), the `key` must match the executable name (e.g., `"cursor-agent"` not `"cursor"`). `shutil.which(key)` is used for CLI tool checks — mismatches require special-case mappings. IDE-based integrations (`requires_cli: False`) are not subject to this constraint.
-2. **Forgetting context configuration**: The bundled `agent-context` extension reads from `.specify/extensions/agent-context/agent-context-config.yml`. New integrations only need to set `context_file` on the class — markers and dispatcher scripts are managed centrally.
+2. **Reintroducing context handling into the CLI**: The opt-in `agent-context` extension owns everything about context files — including the per-agent default mapping in `agent-context-defaults.json`. Integration classes must **not** declare a `context_file`, and no CLI code should read, write, resolve, or migrate context files. All context-file logic lives in `.specify/extensions/agent-context/` and its bundled scripts.
 3. **Incorrect `requires_cli` value**: Set to `True` only for agents that have a CLI tool; set to `False` for IDE-based agents.
 4. **Wrong argument format**: Use `$ARGUMENTS` for Markdown agents, `{{args}}` for TOML agents.
 5. **Skipping registration**: The import and `_register()` call in `_register_builtins()` must both be added.

CHANGELOG.md

@@ -2,6 +2,10 @@
 
 <!-- insert new changelog below this comment -->
 
+### Changed
+
+- feat!: make the `agent-context` extension a full opt-in. `specify init` no longer installs the extension or writes `agent-context-config.yml`, and the Specify CLI no longer creates, updates, removes, resolves, or migrates the managed Spec Kit section in agent context files (e.g. `CLAUDE.md`, `AGENTS.md`, `.github/copilot-instructions.md`). All agent-context knowledge has been removed from the CLI — integration classes no longer declare a `context_file`, and the per-agent default mapping now ships with the extension itself as `agent-context-defaults.json`. The bundled `agent-context` extension fully owns this lifecycle and self-seeds from its own defaults map; install/enable it to manage the context section. Removed the obsolete inline agent-context deprecation warning. Existing projects keep working: previously written sections and config files are left intact and only updated by the extension.
+
 ## [0.11.4] - 2026-06-22
 
 ### Changed

extensions/agent-context/README.md

@@ -6,10 +6,10 @@ It owns the lifecycle of the managed section delimited by the configurable start
 
 ## Why an extension?
 
-Not every Spec Kit user wants Spec Kit to write into the coding agent's context file. Extracting this behavior into a dedicated extension lets users:
+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:
 
-- **Opt out** entirely with `specify extension disable agent-context` — Spec Kit will then never create or modify the agent context file.
-- **Customize the markers** by editing `.specify/extensions/agent-context/agent-context-config.yml` — both the Python layer and the bundled scripts honor the same `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; 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.
 - **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** with `/speckit.agent-context.update`, or automatically through the hooks declared in `extension.yml` (`after_specify`, `after_plan`).
 
@@ -40,7 +40,7 @@ context_markers:
   end: "<!-- SPECKIT END -->"
 ```
 
-- `context_file` — the project-relative path to the coding agent context file, written by `specify init` and `specify integration install`.
+- `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.
 
@@ -62,5 +62,4 @@ pip install pyyaml
 specify extension disable agent-context
 ```
 
-When disabled, Spec Kit skips context file creation, updates, and removal (the gates are inside `upsert_context_section()` and `remove_context_section()`).
-Disabled projects also ignore stale `context_files` values during command rendering so disabling the extension remains a complete opt-out.
+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.

extensions/agent-context/agent-context-defaults.json

@@ -0,0 +1,40 @@
+{
+  "_comment": "Default coding agent context file per integration, owned by the agent-context extension. Used to self-seed agent-context-config.yml when it declares no context_file/context_files. Keyed by the Spec Kit integration key recorded in .specify/init-options.json. This mapping is independent of the Specify CLI by design.",
+  "agents": {
+    "agy": "AGENTS.md",
+    "amp": "AGENTS.md",
+    "auggie": ".augment/rules/specify-rules.md",
+    "bob": "AGENTS.md",
+    "claude": "CLAUDE.md",
+    "cline": ".clinerules/specify-rules.md",
+    "codebuddy": "CODEBUDDY.md",
+    "codex": "AGENTS.md",
+    "copilot": ".github/copilot-instructions.md",
+    "cursor-agent": ".cursor/rules/specify-rules.mdc",
+    "devin": "AGENTS.md",
+    "forge": "AGENTS.md",
+    "gemini": "GEMINI.md",
+    "generic": "AGENTS.md",
+    "goose": "AGENTS.md",
+    "hermes": "AGENTS.md",
+    "iflow": "IFLOW.md",
+    "junie": ".junie/AGENTS.md",
+    "kilocode": ".kilocode/rules/specify-rules.md",
+    "kimi": "KIMI.md",
+    "kiro-cli": "AGENTS.md",
+    "lingma": ".lingma/rules/specify-rules.md",
+    "opencode": "AGENTS.md",
+    "pi": "AGENTS.md",
+    "qodercli": "QODER.md",
+    "qwen": "QWEN.md",
+    "roo": ".roo/rules/specify-rules.md",
+    "rovodev": "AGENTS.md",
+    "shai": "SHAI.md",
+    "tabnine": "TABNINE.md",
+    "trae": ".trae/rules/project_rules.md",
+    "vibe": "AGENTS.md",
+    "windsurf": ".windsurf/rules/specify-rules.md",
+    "zcode": "ZCODE.md",
+    "zed": "AGENTS.md"
+  }
+}

extensions/agent-context/scripts/bash/update-agent-context.sh

@@ -59,7 +59,7 @@ case "$(uname -s 2>/dev/null || true)" in
 esac
 
 # Parse extension config once; emit context files as JSON, followed by marker strings.
-if ! _raw_opts="$("$_python" - "$EXT_CONFIG" "$_case_insensitive_context_files" <<'PY'
+if ! _raw_opts="$("$_python" - "$EXT_CONFIG" "$_case_insensitive_context_files" "$PROJECT_ROOT" <<'PY'
 import json
 import sys
 try:
@@ -95,24 +95,64 @@ def get_str(obj, *keys):
 context_files = []
 seen_context_files = set()
 case_insensitive = sys.argv[2] == "1" or sys.platform.startswith(("win32", "cygwin"))
+def add_context_file(value):
+    if not isinstance(value, str):
+        return
+    candidate = value.strip()
+    if not candidate:
+        return
+    key = candidate.casefold() if case_insensitive else candidate
+    if key in seen_context_files:
+        return
+    context_files.append(candidate)
+    seen_context_files.add(key)
 raw_files = data.get("context_files")
 if isinstance(raw_files, list):
     for value in raw_files:
-        if not isinstance(value, str):
-            continue
-        candidate = value.strip()
-        if not candidate:
-            continue
-        key = candidate.casefold() if case_insensitive else candidate
-        if key in seen_context_files:
-            continue
-        context_files.append(candidate)
-        seen_context_files.add(key)
+        add_context_file(value)
 if not context_files:
-    raw_file = get_str(data, "context_file")
-    candidate = raw_file.strip()
-    if candidate:
-        context_files.append(candidate)
+    add_context_file(get_str(data, "context_file"))
+if not context_files:
+    # Self-seed: the agent-context extension owns its lifecycle, so when its
+    # own config declares no target it derives one from the active integration
+    # recorded in init-options.json, using the extension's OWN bundled mapping
+    # (agent-context-defaults.json). This is independent of the Specify CLI by
+    # design — nothing here imports specify_cli.
+    project_root = sys.argv[3] if len(sys.argv) > 3 else "."
+    integration_key = ""
+    try:
+        with open(
+            f"{project_root}/.specify/init-options.json", "r", encoding="utf-8"
+        ) as fh:
+            opts = json.load(fh)
+        if isinstance(opts, dict):
+            integration_key = opts.get("integration") or opts.get("ai") or ""
+    except Exception:
+        integration_key = ""
+    if integration_key:
+        defaults_path = (
+            f"{project_root}/.specify/extensions/agent-context/"
+            "agent-context-defaults.json"
+        )
+        mapping = {}
+        try:
+            with open(defaults_path, "r", encoding="utf-8") as fh:
+                mapping = (json.load(fh) or {}).get("agents", {})
+        except Exception:
+            print(
+                "agent-context: unable to read %s; cannot self-seed the context "
+                "file. Set 'context_file' in the extension config." % defaults_path,
+                file=sys.stderr,
+            )
+            mapping = {}
+        add_context_file(mapping.get(integration_key, "") or "")
+        if not context_files:
+            print(
+                "agent-context: no default context file is known for integration "
+                "'%s'. Set 'context_file' in the extension config to choose one."
+                % integration_key,
+                file=sys.stderr,
+            )
 print(json.dumps(context_files))
 print(get_str(data, "context_markers", "start"))
 print(get_str(data, "context_markers", "end"))

extensions/agent-context/scripts/powershell/update-agent-context.ps1

@@ -234,6 +234,43 @@ foreach ($ContextFile in $ContextFiles) {
     }
 }
 $ContextFiles = $dedupedContextFiles
+if ($ContextFiles.Count -eq 0) {
+    # Self-seed: the agent-context extension owns its lifecycle, so when its
+    # own config declares no target it derives one from the active integration
+    # recorded in init-options.json, using the extension's OWN bundled mapping
+    # (agent-context-defaults.json). Independent of the Specify CLI by design.
+    $initOptionsPath = Join-Path $ProjectRoot '.specify/init-options.json'
+    if (Test-Path -LiteralPath $initOptionsPath) {
+        try {
+            $initOpts = Get-Content -LiteralPath $initOptionsPath -Raw | ConvertFrom-Json -ErrorAction Stop
+            $integrationKey = $null
+            if ($initOpts.PSObject.Properties['integration'] -and $initOpts.integration) {
+                $integrationKey = [string]$initOpts.integration
+            } elseif ($initOpts.PSObject.Properties['ai'] -and $initOpts.ai) {
+                $integrationKey = [string]$initOpts.ai
+            }
+            if ($integrationKey) {
+                $defaultsPath = Join-Path $ProjectRoot '.specify/extensions/agent-context/agent-context-defaults.json'
+                if (Test-Path -LiteralPath $defaultsPath) {
+                    $defaults = Get-Content -LiteralPath $defaultsPath -Raw | ConvertFrom-Json -ErrorAction Stop
+                    $derived = $null
+                    if ($defaults.PSObject.Properties['agents'] -and $defaults.agents.PSObject.Properties[$integrationKey]) {
+                        $derived = [string]$defaults.agents.$integrationKey
+                    }
+                    if ($derived -and -not [string]::IsNullOrWhiteSpace($derived)) {
+                        $ContextFiles += $derived.Trim()
+                    } else {
+                        Write-Warning ("agent-context: no default context file is known for integration '{0}'; set 'context_file' in the extension config to choose one." -f $integrationKey)
+                    }
+                } else {
+                    Write-Warning ("agent-context: unable to read {0}; cannot self-seed the context file. Set 'context_file' in the extension config." -f $defaultsPath)
+                }
+            }
+        } catch {
+            # Non-fatal: fall through to the nothing-to-do guard below.
+        }
+    }
+}
 if ($ContextFiles.Count -eq 0) {
     Write-Warning 'agent-context: context_files/context_file not set in extension config; nothing to do.'
     exit 0