docs(cli): align init help with bundled scaffolding

Potential fix for pull request finding

Update command package documentation and init help text to reflect the current implementation: init uses bundled assets and integration setup, while placeholder command modules are import anchors until extracted. Remove the unused tracker-active flag assignment that had no reader in the codebase.

Constraint: --offline is hidden/no-op and init no longer downloads templates from GitHub releases

Rejected: Add no-op register functions to placeholder modules | would imply extracted command groups are implemented there

Confidence: high

Scope-risk: narrow

Directive: Keep CLI help text aligned with the actual init scaffolding path

Tested: uv run specify init --help; uv run pytest tests/test_commands_package.py tests/test_agent_config_consistency.py -q; uv run pytest tests/test_commands_package.py tests/test_console_imports.py tests/integrations/test_cli.py -q

Not-tested: full test suite

Author: darion-yaphet

src/specify_cli/commands/__init__.py

@@ -1,2 +1,7 @@
-"""CLI command groups — each module exposes a register(app) function."""
+"""CLI command groups extracted from the main application.
+
+Implemented command modules expose a ``register(app)`` function. Placeholder
+modules are import-only anchors for command groups that still live in the main
+application module.
+"""
 from __future__ import annotations

src/specify_cli/commands/init.py

@@ -105,7 +105,7 @@ def init(
         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)"),
         skip_tls: bool = typer.Option(False, "--skip-tls", help="Deprecated (no-op). Previously: skip SSL/TLS verification.", hidden=True),
-        debug: bool = typer.Option(False, "--debug", help="Deprecated (no-op). Previously: show verbose diagnostic output.", hidden=True),
+        debug: bool = typer.Option(False, "--debug", help="Deprecated. Previously: show verbose diagnostic output; currently only prints additional diagnostic details on failure.", hidden=True),
         github_token: str = typer.Option(None, "--github-token", help="Deprecated (no-op). Previously: GitHub token for API requests.", hidden=True),
         ai_skills: bool = typer.Option(False, "--ai-skills", help="Install Prompt.MD templates as agent skills (requires --ai)"),
         offline: bool = typer.Option(False, "--offline", help="Deprecated (no-op). All scaffolding now uses bundled assets.", hidden=True),
@@ -117,24 +117,18 @@ def init(
         """
         Initialize a new Specify project.
 
-        By default, project files are downloaded from the latest GitHub release.
-        Use --offline to scaffold from assets bundled inside the specify-cli
-        package instead (no internet access required, ideal for air-gapped or
-        enterprise environments).
-
-        NOTE: Starting with v0.6.0, bundled assets will be used by default and
-        the --offline flag will be removed. The GitHub download path will be
-        retired because bundled assets eliminate the need for network access,
-        avoid proxy/firewall issues, and guarantee that templates always match
-        the installed CLI version.
+        Project files are scaffolded from assets bundled inside the specify-cli
+        package, so initialization does not need network access and templates
+        match the installed CLI version.
 
         This command will:
         1. Check that required tools are installed (git is optional)
         2. Let you choose your coding agent integration, or default to Copilot
            in non-interactive sessions
-        3. Download template from GitHub (or use bundled assets with --offline)
+        3. Install bundled Spec Kit templates, scripts, workflow, and shared
+           project infrastructure
         4. Initialize a fresh git repository (if not --no-git and no existing repo)
-        5. Optionally set up coding agent integration commands
+        5. Set up coding agent integration commands and optional presets
 
         Examples:
             specify init my-project
@@ -384,8 +378,6 @@ def init(
 
         tracker = StepTracker("Initialize Specify Project")
 
-        sys._specify_tracker_active = True
-
         tracker.add("precheck", "Check required tools")
         tracker.complete("precheck", "ok")
         tracker.add("ai-select", "Select coding agent integration")