docs: replace deprecated --ai flag with --integration in all documentation (#2359)

* docs: replace deprecated --ai flag with --integration in all documentation

Replace all user-facing --ai, --ai-skills, and --ai-commands-dir references
with their modern equivalents:

- --ai <agent> → --integration <agent>
- --ai-skills → --integration-options="--skills"
- --ai-commands-dir <dir> → --integration generic --integration-options="--commands-dir <dir>"

Updated files:
- README.md (~17 occurrences)
- docs/installation.md (~8 occurrences)
- docs/upgrade.md (~11 occurrences)
- docs/local-development.md (~5 occurrences)
- CONTRIBUTING.md (1 occurrence)
- extensions/EXTENSION-USER-GUIDE.md (1 occurrence)
- src/specify_cli/__init__.py (docstring examples and error messages)

Left unchanged:
- CHANGELOG.md (historical record)
- Test files (intentionally exercise deprecated flag path)
- CLI flag implementation (backward compatibility)

Closes #2358

* docs: address review feedback on pre-existing issues

- Fix duplicate copilot example in README.md (replace with codex)
- Fix invalid gemini --integration-options="--skills" example (gemini
  does not support --skills)
- Update generic integration comment from 'Unsupported agent' to
  'Bring your own agent; requires --commands-dir'
- Clarify EXTENSION-USER-GUIDE.md: skills auto-register for
  skills-based integrations, not only with --integration-options

* docs: replace bare 'AI agent' / 'AI assistant' with 'coding agent' throughout

Full sweep across all documentation and user-facing CLI messages to
align terminology. Bare references like 'AI agent', 'AI assistant',
and 'AI Agent' are replaced with 'coding agent' or 'coding agent
integration' as appropriate.

Intentionally left unchanged:
- 'AI coding agent' (already correct expanded form)
- Deprecated --ai flag help text and error messages (describes the
  deprecated flag itself)
- Community extension descriptions (external project text)
- 'generated by an AI' in CONTRIBUTING.md (general AI, not agent)

* docs: address review — remove deprecated --offline, qualify --skills scope

- Remove --offline from docstring examples (deprecated no-op)
- Remove --offline from CONTRIBUTING.md testing example
- Replace --offline instructions in docs/installation.md with note that
  bundled assets are used by default
- Qualify --integration-options="--skills" in README.md to note it only
  applies to integrations that support skills mode

src/specify_cli/__init__.py

@@ -967,7 +967,7 @@ def init(
     ai_assistant: str = typer.Option(None, "--ai", help=AI_ASSISTANT_HELP),
     ai_commands_dir: str = typer.Option(None, "--ai-commands-dir", help="Directory for agent command files (required with --ai generic, e.g. .myagent/commands/)"),
     script_type: str = typer.Option(None, "--script", help="Script type to use: sh or ps"),
-    ignore_agent_tools: bool = typer.Option(False, "--ignore-agent-tools", help="Skip checks for AI agent tools like Claude Code"),
+    ignore_agent_tools: bool = typer.Option(False, "--ignore-agent-tools", help="Skip checks for coding agent tools like Claude Code"),
     no_git: bool = typer.Option(False, "--no-git", help="Skip git repository initialization"),
     here: bool = typer.Option(False, "--here", help="Initialize project in the current directory instead of creating a new one"),
     force: bool = typer.Option(False, "--force", help="Force merge/overwrite when using --here (skip confirmation)"),
@@ -997,29 +997,28 @@ def init(
 
     This command will:
     1. Check that required tools are installed (git is optional)
-    2. Let you choose your AI assistant
+    2. Let you choose your coding agent integration
     3. Download template from GitHub (or use bundled assets with --offline)
     4. Initialize a fresh git repository (if not --no-git and no existing repo)
-    5. Optionally set up AI assistant commands
+    5. Optionally set up coding agent integration commands
 
     Examples:
         specify init my-project
-        specify init my-project --ai claude
-        specify init my-project --ai copilot --no-git
+        specify init my-project --integration claude
+        specify init my-project --integration copilot --no-git
         specify init --ignore-agent-tools my-project
-        specify init . --ai claude         # Initialize in current directory
-        specify init .                     # Initialize in current directory (interactive AI selection)
-        specify init --here --ai claude    # Alternative syntax for current directory
-        specify init --here --ai codex --ai-skills
-        specify init --here --ai codebuddy
-        specify init --here --ai vibe      # Initialize with Mistral Vibe support
+        specify init . --integration claude         # Initialize in current directory
+        specify init .                     # Initialize in current directory (interactive integration selection)
+        specify init --here --integration claude    # Alternative syntax for current directory
+        specify init --here --integration codex --integration-options="--skills"
+        specify init --here --integration codebuddy
+        specify init --here --integration vibe      # Initialize with Mistral Vibe support
         specify init --here
         specify init --here --force  # Skip confirmation when current directory not empty
-        specify init my-project --ai claude   # Claude installs skills by default
-        specify init --here --ai gemini --ai-skills
-        specify init my-project --ai generic --ai-commands-dir .myagent/commands/  # Unsupported agent
-        specify init my-project --offline  # Use bundled assets (no network access)
-        specify init my-project --ai claude --preset healthcare-compliance  # With preset
+        specify init my-project --integration claude   # Claude installs skills by default
+        specify init --here --integration gemini
+        specify init my-project --integration generic --integration-options="--commands-dir .myagent/commands/"  # Bring your own agent; requires --commands-dir
+        specify init my-project --integration claude --preset healthcare-compliance  # With preset
     """
 
     show_banner()
@@ -1029,14 +1028,14 @@ def init(
     if ai_assistant and ai_assistant.startswith("--"):
         console.print(f"[red]Error:[/red] Invalid value for --ai: '{ai_assistant}'")
         console.print("[yellow]Hint:[/yellow] Did you forget to provide a value for --ai?")
-        console.print("[yellow]Example:[/yellow] specify init --ai claude --here")
+        console.print("[yellow]Example:[/yellow] specify init --integration claude --here")
         console.print(f"[yellow]Available agents:[/yellow] {', '.join(AGENT_CONFIG.keys())}")
         raise typer.Exit(1)
 
     if ai_commands_dir and ai_commands_dir.startswith("--"):
         console.print(f"[red]Error:[/red] Invalid value for --ai-commands-dir: '{ai_commands_dir}'")
         console.print("[yellow]Hint:[/yellow] Did you forget to provide a value for --ai-commands-dir?")
-        console.print("[yellow]Example:[/yellow] specify init --ai generic --ai-commands-dir .myagent/commands/")
+        console.print("[yellow]Example:[/yellow] specify init --integration generic --integration-options=\"--commands-dir .myagent/commands/\"")
         raise typer.Exit(1)
 
     if ai_assistant:
@@ -1170,7 +1169,7 @@ def init(
         ai_choices = {key: config["name"] for key, config in AGENT_CONFIG.items()}
         selected_ai = select_with_arrows(
             ai_choices,
-            "Choose your AI assistant:",
+            "Choose your coding agent integration:",
             "copilot"
         )
 
@@ -1241,7 +1240,7 @@ def init(
         else:
             selected_script = default_script
 
-    console.print(f"[cyan]Selected AI assistant:[/cyan] {selected_ai}")
+    console.print(f"[cyan]Selected coding agent integration:[/cyan] {selected_ai}")
     console.print(f"[cyan]Selected script type:[/cyan] {selected_script}")
 
     tracker = StepTracker("Initialize Specify Project")
@@ -1250,7 +1249,7 @@ def init(
 
     tracker.add("precheck", "Check required tools")
     tracker.complete("precheck", "ok")
-    tracker.add("ai-select", "Select AI assistant")
+    tracker.add("ai-select", "Select coding agent integration")
     tracker.complete("ai-select", f"{selected_ai}")
     tracker.add("script-select", "Select script type")
     tracker.complete("script-select", selected_script)
@@ -1565,7 +1564,7 @@ def init(
             return f"/speckit-{name}"
         return f"/speckit.{name}"
 
-    steps_lines.append(f"{step_num}. Start using {usage_label} with your AI agent:")
+    steps_lines.append(f"{step_num}. Start using {usage_label} with your coding agent:")
 
     steps_lines.append(f"   {step_num}.1 [cyan]{_display_cmd('constitution')}[/] - Establish project principles")
     steps_lines.append(f"   {step_num}.2 [cyan]{_display_cmd('specify')}[/] - Create baseline specification")
@@ -1636,7 +1635,7 @@ def check():
         console.print("[dim]Tip: Install git for repository management[/dim]")
 
     if not any(agent_results.values()):
-        console.print("[dim]Tip: Install an AI assistant for the best experience[/dim]")
+        console.print("[dim]Tip: Install a coding agent for the best experience[/dim]")
 
 @app.command()
 def version():
@@ -1882,7 +1881,7 @@ def get_speckit_version() -> str:
 
 integration_app = typer.Typer(
     name="integration",
-    help="Manage AI agent integrations",
+    help="Manage coding agent integrations",
     add_completion=False,
 )
 app.add_typer(integration_app, name="integration")
@@ -2020,7 +2019,7 @@ def integration_list(
         console.print(table)
         return
 
-    table = Table(title="AI Agent Integrations")
+    table = Table(title="Coding Agent Integrations")
     table.add_column("Key", style="cyan")
     table.add_column("Name")
     table.add_column("Status")