Update Markdown formatting

docs: Add existing project initialization to getting started

AGENTS.md

@@ -30,7 +30,7 @@ Specify supports multiple AI agents by generating agent-specific command files a
 ### Current Supported Agents
 
 | Agent                      | Directory              | Format   | CLI Tool        | Description                 |
-|-------|-----------|---------|----------|-------------|
+| -------------------------- | ---------------------- | -------- | --------------- | --------------------------- |
 | **Claude Code**            | `.claude/commands/`    | Markdown | `claude`        | Anthropic's Claude Code CLI |
 | **Gemini CLI**             | `.gemini/commands/`    | TOML     | `gemini`        | Google's Gemini CLI         |
 | **GitHub Copilot**         | `.github/agents/`      | Markdown | N/A (IDE-based) | GitHub Copilot in VS Code   |

CONTRIBUTING.md

@@ -71,13 +71,13 @@ To test your templates, commands, and other changes locally, follow these steps:
 
    Run the following command to generate the local packages:
 
-   ```
+   ```bash
    ./.github/workflows/scripts/create-release-packages.sh v1.0.0
    ```
 
 2. **Copy the relevant package to your test project**
 
-   ```
+   ```bash
    cp -r .genreleases/sdd-copilot-package-sh/. <path-to-test-project>/
    ```
 

README.md

@@ -57,7 +57,15 @@ uv tool install specify-cli --from git+https://github.com/github/spec-kit.git
 Then use the tool directly:
 
 ```bash
+# Create new project
 specify init <PROJECT_NAME>
+
+# Or initialize in existing project
+specify init . --ai claude
+# or
+specify init --here --ai claude
+
+# Check installed tools
 specify check
 ```
 
@@ -135,7 +143,7 @@ Want to see Spec Kit in action? Watch our [video overview](https://www.youtube.c
 ## 🤖 Supported AI Agents
 
 | Agent                                                                                | Support | Notes                                                                                                                                     |
-|-----------------------------------------------------------|---------|---------------------------------------------------|
+| ------------------------------------------------------------------------------------ | ------- | ----------------------------------------------------------------------------------------------------------------------------------------- |
 | [Qoder CLI](https://qoder.com/cli)                                                   | ✅      |                                                                                                                                           |
 | [Amazon Q Developer CLI](https://aws.amazon.com/developer/learning/q-developer-cli/) | ⚠️      | Amazon Q Developer CLI [does not support](https://github.com/aws/amazon-q-developer-cli/issues/3064) custom arguments for slash commands. |
 | [Amp](https://ampcode.com/)                                                          | ✅      |                                                                                                                                           |
@@ -162,14 +170,14 @@ The `specify` command supports the following options:
 ### Commands
 
 | Command | Description                                                                                                                                             |
-|-------------|----------------------------------------------------------------|
+| ------- | ------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | `init`  | Initialize a new Specify project from the latest template                                                                                               |
 | `check` | Check for installed tools (`git`, `claude`, `gemini`, `code`/`code-insiders`, `cursor-agent`, `windsurf`, `qwen`, `opencode`, `codex`, `shai`, `qoder`) |
 
 ### `specify init` Arguments & Options
 
 | Argument/Option        | Type     | Description                                                                                                                                                                                  |
-|------------------------|----------|------------------------------------------------------------------------------|
+| ---------------------- | -------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | `<project-name>`       | Argument | Name for your new project directory (optional if using `--here`, or use `.` for current directory)                                                                                           |
 | `--ai`                 | Option   | AI assistant to use: `claude`, `gemini`, `copilot`, `cursor-agent`, `qwen`, `opencode`, `codex`, `windsurf`, `kilocode`, `auggie`, `roo`, `codebuddy`, `amp`, `shai`, `q`, `bob`, or `qoder` |
 | `--script`             | Option   | Script variant to use: `sh` (bash/zsh) or `ps` (PowerShell)                                                                                                                                  |
@@ -243,7 +251,7 @@ After running `specify init`, your AI coding agent will have access to these sla
 Essential commands for the Spec-Driven Development workflow:
 
 | Command                 | Description                                                              |
-|--------------------------|-----------------------------------------------------------------------|
+| ----------------------- | ------------------------------------------------------------------------ |
 | `/speckit.constitution` | Create or update project governing principles and development guidelines |
 | `/speckit.specify`      | Define what you want to build (requirements and user stories)            |
 | `/speckit.plan`         | Create technical implementation plans with your chosen tech stack        |
@@ -255,7 +263,7 @@ Essential commands for the Spec-Driven Development workflow:
 Additional commands for enhanced quality and validation:
 
 | Command              | Description                                                                                                                          |
-|----------------------|-----------------------------------------------------------------------|
+| -------------------- | ------------------------------------------------------------------------------------------------------------------------------------ |
 | `/speckit.clarify`   | Clarify underspecified areas (recommended before `/speckit.plan`; formerly `/quizme`)                                                |
 | `/speckit.analyze`   | Cross-artifact consistency & coverage analysis (run after `/speckit.tasks`, before `/speckit.implement`)                             |
 | `/speckit.checklist` | Generate custom quality checklists that validate requirements completeness, clarity, and consistency (like "unit tests for English") |
@@ -263,8 +271,8 @@ Additional commands for enhanced quality and validation:
 ### Environment Variables
 
 | Variable          | Description                                                                                                                                                                                                                                                                                            |
-|------------------|------------------------------------------------------------------------------------------------|
+| ----------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
-| `SPECIFY_FEATURE` | Override feature detection for non-Git repositories. Set to the feature directory name (e.g., `001-photo-albums`) to work on a specific feature when not using Git branches.<br/>**Must be set in the context of the agent you're working with prior to using `/speckit.plan` or follow-up commands. |
+| `SPECIFY_FEATURE` | Override feature detection for non-Git repositories. Set to the feature directory name (e.g., `001-photo-albums`) to work on a specific feature when not using Git branches.<br/>\*\*Must be set in the context of the agent you're working with prior to using `/speckit.plan` or follow-up commands. |
 
 ## 📚 Core Philosophy
 
@@ -278,7 +286,7 @@ Spec-Driven Development is a structured process that emphasizes:
 ## 🌟 Development Phases
 
 | Phase                                    | Focus                    | Key Activities                                                                                                                                                     |
-|-------|-------|----------------|
+| ---------------------------------------- | ------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
 | **0-to-1 Development** ("Greenfield")    | Generate from scratch    | <ul><li>Start with high-level requirements</li><li>Generate specifications</li><li>Plan implementation steps</li><li>Build production-ready applications</li></ul> |
 | **Creative Exploration**                 | Parallel implementations | <ul><li>Explore diverse solutions</li><li>Support multiple technology stacks & architectures</li><li>Experiment with UX patterns</li></ul>                         |
 | **Iterative Enhancement** ("Brownfield") | Brownfield modernization | <ul><li>Add features iteratively</li><li>Modernize legacy systems</li><li>Adapt processes</li></ul>                                                                |

docs/upgrade.md

@@ -86,7 +86,7 @@ specify init --here --force --ai copilot
 
 Without `--force`, the CLI warns you and asks for confirmation:
 
-```
+```text
 Warning: Current directory is not empty (25 items)
 Template files will be merged with existing content and may overwrite existing files
 Proceed? [y/N]
@@ -286,11 +286,13 @@ This tells Spec Kit which feature directory to use when creating specs, plans, a
 
 1. **Restart your IDE/editor** completely (not just reload window)
 2. **For CLI-based agents**, verify files exist:
+
    ```bash
    ls -la .claude/commands/      # Claude Code
    ls -la .gemini/commands/       # Gemini
    ls -la .cursor/commands/       # Cursor
    ```
+
 3. **Check agent-specific setup:**
    - Codex requires `CODEX_HOME` environment variable
    - Some agents need workspace restart or cache clearing
@@ -312,7 +314,8 @@ cp /tmp/constitution-backup.md .specify/memory/constitution.md
 ### "Warning: Current directory is not empty"
 
 **Full warning message:**
-```
+
+```text
 Warning: Current directory is not empty (25 items)
 Template files will be merged with existing content and may overwrite existing files
 Do you want to continue? [y/N]
@@ -329,6 +332,7 @@ This warning appears when you run `specify init --here` (or `specify init .`) in
 **What gets overwritten:**
 
 Only Spec Kit infrastructure files:
+
 - Agent command files (`.claude/commands/`, `.github/prompts/`, etc.)
 - Scripts in `.specify/scripts/`
 - Templates in `.specify/templates/`
@@ -346,6 +350,7 @@ Only Spec Kit infrastructure files:
 - **Type `y` and press Enter** - Proceed with the merge (recommended if upgrading)
 - **Type `n` and press Enter** - Cancel the operation
 - **Use `--force` flag** - Skip this confirmation entirely:
+
   ```bash
   specify init --here --force --ai copilot
   ```
@@ -388,6 +393,7 @@ uv tool install specify-cli --from git+https://github.com/github/spec-kit.git
 **Explanation:**
 
 The `specify` CLI tool is used for:
+
 - **Initial setup:** `specify init` to bootstrap Spec Kit in your project
 - **Upgrades:** `specify init --here --force` to update templates and commands
 - **Diagnostics:** `specify check` to verify tool installation
@@ -397,6 +403,7 @@ Once you've run `specify init`, the slash commands (like `/speckit.specify`, `/s
 **If your agent isn't recognizing slash commands:**
 
 1. **Verify command files exist:**
+
    ```bash
    # For GitHub Copilot
    ls -la .github/prompts/
@@ -412,6 +419,7 @@ Once you've run `specify init`, the slash commands (like `/speckit.specify`, `/s
 4. **For some agents**, you may need to reload the workspace or clear cache
 
 **Related issue:** If Copilot can't open local files or uses PowerShell commands unexpectedly, this is typically an IDE context issue, not related to `specify`. Try:
+
 - Restarting VS Code
 - Checking file permissions
 - Ensuring the workspace folder is properly opened

spec-driven.md

@@ -195,6 +195,7 @@ The templates include comprehensive checklists that act as "unit tests" for the
 
 ```markdown
 ### Requirement Completeness
+
 - [ ] No [NEEDS CLARIFICATION] markers remain
 - [ ] Requirements are testable and unambiguous
 - [ ] Success criteria are measurable
@@ -208,10 +209,14 @@ The implementation plan template enforces architectural principles through phase
 
 ```markdown
 ### Phase -1: Pre-Implementation Gates
+
 #### Simplicity Gate (Article VII)
+
 - [ ] Using ≤3 projects?
 - [ ] No future-proofing?
+
 #### Anti-Abstraction Gate (Article VIII)
+
 - [ ] Using framework directly?
 - [ ] Single model representation?
 ```
@@ -347,15 +352,19 @@ The implementation plan template operationalizes these articles through concrete
 
 ```markdown
 ### Phase -1: Pre-Implementation Gates
+
 #### Simplicity Gate (Article VII)
+
 - [ ] Using ≤3 projects?
 - [ ] No future-proofing?
 
 #### Anti-Abstraction Gate (Article VIII)
+
 - [ ] Using framework directly?
 - [ ] Single model representation?
 
 #### Integration-First Gate (Article IX)
+
 - [ ] Contracts defined?
 - [ ] Contract tests written?
 ```

templates/commands/specify.md

@@ -42,6 +42,7 @@ Given that feature description, do this:
 2. **Check for existing branches before creating new one**:
 
    a. First, fetch all remote branches to ensure we have the latest information:
+
       ```bash
       git fetch --all --prune
       ```

templates/commands/taskstoissues.md

@@ -24,8 +24,10 @@ You **MUST** consider the user input before proceeding (if not empty).
 git config --get remote.origin.url
 ```
 
-**ONLY PROCEED TO NEXT STEPS IF THE REMOTE IS A GITHUB URL**
+> [!CAUTION]
+> ONLY PROCEED TO NEXT STEPS IF THE REMOTE IS A GITHUB URL
 
 1. For each task in the list, use the GitHub MCP server to create a new issue in the repository that is representative of the Git remote.
 
-**UNDER NO CIRCUMSTANCES EVER CREATE ISSUES IN REPOSITORIES THAT DO NOT MATCH THE REMOTE URL**
+> [!CAUTION]
+> UNDER NO CIRCUMSTANCES EVER CREATE ISSUES IN REPOSITORIES THAT DO NOT MATCH THE REMOTE URL