docs: add workflows reference, reorganize into docs/reference/, and add --version flag (#2244)

* docs: add workflows reference, reorganize into docs/reference/, and add --version flag

- Move integrations.md, extensions.md, presets.md into docs/reference/
- New docs/reference/workflows.md: command reference for all workflow
  commands, built-in SDD Cycle workflow with Mermaid diagram, step types,
  expressions, input types, state/resume, and FAQ
- Rename workflow input feature_name to spec with prompt 'Describe what
  you want to build' to match speckit.specify command terminology
- Add --version / -V flag to root specify command with tests
- Update docs/toc.yml, README.md links, and docs/upgrade.md cross-reference
  to use reference/ paths
- Add workflow command to README CLI reference table

* docs: update speckit_version requirement to >=0.7.2 in workflow example

Author: mnriem

README.md

@@ -316,7 +316,7 @@ Community projects that extend, visualize, or build on Spec Kit:
 
 ## 🤖 Supported AI Coding Agent Integrations
 
-Spec Kit works with 30+ AI coding agents — both CLI tools and IDE-based assistants. See the full list with notes and usage details in the [Supported AI Coding Agent Integrations](https://github.github.io/spec-kit/integrations.html) guide.
+Spec Kit works with 30+ AI coding agents — both CLI tools and IDE-based assistants. See the full list with notes and usage details in the [Supported AI Coding Agent Integrations](https://github.github.io/spec-kit/reference/integrations.html) guide.
 
 Run `specify integration list` to see all available integrations in your installed version.
 
@@ -367,6 +367,7 @@ and supports the following commands:
 | `extension`   | Manage extensions                                                                                                                                                                                                                                                                                                                            |
 | `preset`      | Manage presets                                                                                                                                                                                                                                                                                                                               |
 | `integration` | Manage integrations                                                                                                                                                                                                                                                                                                                          |
+| `workflow`    | Run, manage, and search workflows. See the [Workflows reference](https://github.github.io/spec-kit/reference/workflows.html)                                                                                                                                                                                                                |
 
 ### `specify init` Arguments & Options
 
@@ -510,7 +511,7 @@ specify extension add <extension-name>
 
 For example, extensions could add Jira integration, post-implementation code review, V-Model test traceability, or project health diagnostics.
 
-See the [Extensions reference](https://github.github.io/spec-kit/extensions.html) for the full command guide. Browse the [community extensions](#-community-extensions) above for what's available.
+See the [Extensions reference](https://github.github.io/spec-kit/reference/extensions.html) for the full command guide. Browse the [community extensions](#-community-extensions) above for what's available.
 
 ### Presets — Customize Existing Workflows
 
@@ -526,7 +527,7 @@ specify preset add <preset-name>
 
 For example, presets could restructure spec templates to require regulatory traceability, adapt the workflow to fit the methodology you use (e.g., Agile, Kanban, Waterfall, jobs-to-be-done, or domain-driven design), add mandatory security review gates to plans, enforce test-first task ordering, or localize the entire workflow to a different language. The [pirate-speak demo](https://github.com/mnriem/spec-kit-pirate-speak-preset-demo) shows just how deep the customization can go. Multiple presets can be stacked with priority ordering.
 
-See the [Presets reference](https://github.github.io/spec-kit/presets.html) for the full command guide, including resolution order and priority stacking.
+See the [Presets reference](https://github.github.io/spec-kit/reference/presets.html) for the full command guide, including resolution order and priority stacking.
 
 ### When to Use Which
 

docs/extensions.md docs/reference/extensions.mddocs/extensions.md renamed to docs/reference/extensions.md

@@ -0,0 +1,289 @@
+# Workflows
+
+Workflows automate multi-step Spec-Driven Development processes — chaining commands, prompts, shell steps, and human checkpoints into repeatable sequences. They support conditional logic, loops, fan-out/fan-in, and can be paused and resumed from the exact point of interruption.
+
+## Run a Workflow
+
+```bash
+specify workflow run <source>
+```
+
+| Option              | Description                                              |
+| ------------------- | -------------------------------------------------------- |
+| `-i` / `--input`    | Pass input values as `key=value` (repeatable)            |
+
+Runs a workflow from a catalog ID, URL, or local file path. Inputs declared by the workflow can be provided via `--input` or will be prompted interactively.
+
+Example:
+
+```bash
+specify workflow run speckit -i spec="Build a kanban board with drag-and-drop task management" -i scope=full
+```
+
+> **Note:** All workflow commands require a project already initialized with `specify init`.
+
+## Resume a Workflow
+
+```bash
+specify workflow resume <run_id>
+```
+
+Resumes a paused or failed workflow run from the exact step where it stopped. Useful after responding to a gate step or fixing an issue that caused a failure.
+
+## Workflow Status
+
+```bash
+specify workflow status [<run_id>]
+```
+
+Shows the status of a specific run, or lists all runs if no ID is given. Run states: `created`, `running`, `completed`, `paused`, `failed`, `aborted`.
+
+## List Installed Workflows
+
+```bash
+specify workflow list
+```
+
+Lists workflows installed in the current project.
+
+## Install a Workflow
+
+```bash
+specify workflow add <source>
+```
+
+Installs a workflow from the catalog, a URL (HTTPS required), or a local file path.
+
+## Remove a Workflow
+
+```bash
+specify workflow remove <workflow_id>
+```
+
+Removes an installed workflow from the project.
+
+## Search Available Workflows
+
+```bash
+specify workflow search [query]
+```
+
+| Option  | Description     |
+| ------- | --------------- |
+| `--tag` | Filter by tag   |
+
+Searches all active catalogs for workflows matching the query.
+
+## Workflow Info
+
+```bash
+specify workflow info <workflow_id>
+```
+
+Shows detailed information about a workflow, including its steps, inputs, and requirements.
+
+## Catalog Management
+
+Workflow catalogs control where `search` and `add` look for workflows. Catalogs are checked in priority order.
+
+### List Catalogs
+
+```bash
+specify workflow catalog list
+```
+
+Shows all active catalog sources.
+
+### Add a Catalog
+
+```bash
+specify workflow catalog add <url>
+```
+
+| Option          | Description                      |
+| --------------- | -------------------------------- |
+| `--name <name>` | Optional name for the catalog    |
+
+Adds a custom catalog URL to the project's `.specify/workflow-catalogs.yml`.
+
+### Remove a Catalog
+
+```bash
+specify workflow catalog remove <index>
+```
+
+Removes a catalog by its index in the catalog list.
+
+### Catalog Resolution Order
+
+Catalogs are resolved in this order (first match wins):
+
+1. **Environment variable** — `SPECKIT_WORKFLOW_CATALOG_URL` overrides all catalogs
+2. **Project config** — `.specify/workflow-catalogs.yml`
+3. **User config** — `~/.specify/workflow-catalogs.yml`
+4. **Built-in defaults** — official catalog + community catalog
+
+## Workflow Definition
+
+Workflows are defined in YAML files. Here is the built-in **Full SDD Cycle** workflow that ships with Spec Kit:
+
+```yaml
+schema_version: "1.0"
+workflow:
+  id: "speckit"
+  name: "Full SDD Cycle"
+  version: "1.0.0"
+  author: "GitHub"
+  description: "Runs specify → plan → tasks → implement with review gates"
+
+requires:
+  speckit_version: ">=0.7.2"
+  integrations:
+    any: ["copilot", "claude", "gemini"]
+
+inputs:
+  spec:
+    type: string
+    required: true
+    prompt: "Describe what you want to build"
+  integration:
+    type: string
+    default: "copilot"
+    prompt: "Integration to use (e.g. claude, copilot, gemini)"
+  scope:
+    type: string
+    default: "full"
+    enum: ["full", "backend-only", "frontend-only"]
+
+steps:
+  - id: specify
+    command: speckit.specify
+    integration: "{{ inputs.integration }}"
+    input:
+      args: "{{ inputs.spec }}"
+
+  - id: review-spec
+    type: gate
+    message: "Review the generated spec before planning."
+    options: [approve, reject]
+    on_reject: abort
+
+  - id: plan
+    command: speckit.plan
+    integration: "{{ inputs.integration }}"
+    input:
+      args: "{{ inputs.spec }}"
+
+  - id: review-plan
+    type: gate
+    message: "Review the plan before generating tasks."
+    options: [approve, reject]
+    on_reject: abort
+
+  - id: tasks
+    command: speckit.tasks
+    integration: "{{ inputs.integration }}"
+    input:
+      args: "{{ inputs.spec }}"
+
+  - id: implement
+    command: speckit.implement
+    integration: "{{ inputs.integration }}"
+    input:
+      args: "{{ inputs.spec }}"
+```
+
+This produces the following execution flow:
+
+```mermaid
+flowchart TB
+    A["specify<br/>(command)"] --> B{"review-spec<br/>(gate)"}
+    B -- approve --> C["plan<br/>(command)"]
+    B -- reject --> X1["⏹ Abort"]
+    C --> D{"review-plan<br/>(gate)"}
+    D -- approve --> E["tasks<br/>(command)"]
+    D -- reject --> X2["⏹ Abort"]
+    E --> F["implement<br/>(command)"]
+
+    style A fill:#49a,color:#fff
+    style B fill:#a94,color:#fff
+    style C fill:#49a,color:#fff
+    style D fill:#a94,color:#fff
+    style E fill:#49a,color:#fff
+    style F fill:#49a,color:#fff
+    style X1 fill:#999,color:#fff
+    style X2 fill:#999,color:#fff
+```
+
+Run it with:
+
+```bash
+specify workflow run speckit -i spec="Build a kanban board with drag-and-drop task management"
+```
+
+## Step Types
+
+| Type         | Purpose                                          |
+| ------------ | ------------------------------------------------ |
+| `command`    | Invoke a Spec Kit command (e.g., `speckit.plan`) |
+| `prompt`     | Send an arbitrary prompt to the AI coding agent  |
+| `shell`      | Execute a shell command and capture output       |
+| `gate`       | Pause for human approval before continuing       |
+| `if`         | Conditional branching (then/else)                |
+| `switch`     | Multi-branch dispatch on an expression           |
+| `while`      | Loop while a condition is true                   |
+| `do-while`   | Execute at least once, then loop on condition    |
+| `fan-out`    | Dispatch a step for each item in a list          |
+| `fan-in`     | Aggregate results from a fan-out step            |
+
+## Expressions
+
+Steps can reference inputs and previous step outputs using `{{ expression }}` syntax:
+
+| Namespace                      | Description                          |
+| ------------------------------ | ------------------------------------ |
+| `inputs.spec`                  | Workflow input values                |
+| `steps.specify.output.file`    | Output from a previous step          |
+| `item`                         | Current item in a fan-out iteration  |
+
+Available filters: `default`, `join`, `contains`, `map`.
+
+Example:
+
+```yaml
+condition: "{{ steps.test.output.exit_code == 0 }}"
+args: "{{ inputs.spec }}"
+message: "{{ status | default('pending') }}"
+```
+
+## Input Types
+
+| Type      | Coercion                                          |
+| --------- | ------------------------------------------------- |
+| `string`  | Pass-through                                      |
+| `number`  | `"42"` → `42`, `"3.14"` → `3.14`                 |
+| `boolean` | `"true"` / `"1"` / `"yes"` → `True`              |
+
+## State and Resume
+
+Each workflow run persists its state at `.specify/workflows/runs/<run_id>/`:
+
+- `state.json` — current run state and step progress
+- `inputs.json` — resolved input values
+- `log.jsonl` — step-by-step execution log
+
+This enables `specify workflow resume` to continue from the exact step where a run was paused (e.g., at a gate) or failed.
+
+## FAQ
+
+### What happens when a workflow hits a gate step?
+
+The workflow pauses and waits for human input. Run `specify workflow resume <run_id>` after reviewing to continue.
+
+### Can I run the same workflow multiple times?
+
+Yes. Each run gets a unique ID and its own state directory. Use `specify workflow status` to see all runs.
+
+### Who maintains workflows?
+
+Most workflows are independently created and maintained by their respective authors. The Spec Kit maintainers do not review, audit, endorse, or support workflow code. Review a workflow's source before installing and use at your own discretion.

docs/integrations.md docs/reference/integrations.mddocs/integrations.md renamed to docs/reference/integrations.md

@@ -16,11 +16,13 @@
 - name: Reference
   items:
     - name: Integrations
-      href: integrations.md
+      href: reference/integrations.md
     - name: Extensions
-      href: extensions.md
+      href: reference/extensions.md
     - name: Presets
-      href: presets.md
+      href: reference/presets.md
+    - name: Workflows
+      href: reference/workflows.md
 
 # Development workflows
 - name: Development

docs/presets.md docs/reference/presets.mddocs/presets.md renamed to docs/reference/presets.md

@@ -76,7 +76,7 @@ Run this inside your project directory:
 specify init --here --force --ai <your-agent>
 ```
 
-Replace `<your-agent>` with your AI coding agent. Refer to this list of [Supported AI Coding Agent Integrations](integrations.md)
+Replace `<your-agent>` with your AI coding agent. Refer to this list of [Supported AI Coding Agent Integrations](reference/integrations.md)
 
 **Example:**
 

docs/reference/workflows.md

@@ -351,8 +351,16 @@ def show_banner():
     console.print(Align.center(Text(TAGLINE, style="italic bright_yellow")))
     console.print()
 
+def _version_callback(value: bool):
+    if value:
+        console.print(f"specify {get_speckit_version()}")
+        raise typer.Exit()
+
 @app.callback()
-def callback(ctx: typer.Context):
+def callback(
+    ctx: typer.Context,
+    version: bool = typer.Option(False, "--version", "-V", callback=_version_callback, is_eager=True, help="Show version and exit."),
+):
     """Show banner when no subcommand is provided."""
     if ctx.invoked_subcommand is None and "--help" not in sys.argv and "-h" not in sys.argv:
         show_banner()

docs/toc.yml

@@ -255,7 +255,7 @@ def evaluate_expression(template: str, context: Any) -> Any:
     ----------
     template:
         The template string (e.g., ``"{{ steps.plan.output.task_count }}"``
-        or ``"Processed {{ inputs.feature_name }}"``.
+        or ``"Processed {{ inputs.spec }}"``.
     context:
         A ``StepContext`` or compatible object.