Implement complete CLI commands for MVP-1 Personal Tracker

- Refactored CLI commands from nested Typer subapps to direct command functions
- Fixed main.py to use app.command() instead of app.add_typer_command()
- Fixed project_service.py to properly load projects from YAML
- Fixed file_storage.py to save session JSON files alongside markdown
- Added missing methods: write_file, read_file, extract_autogen_section, get_recent_sessions
- Fixed root_path and repo_path to use strings instead of Path objects

tracker/cli/commands.py

@@ -35,11 +35,7 @@ markdown_writer = MarkdownWriter()
 # =============================================================================
 # init-project command
 # =============================================================================
-init_project = typer.Typer(help="Create a new project with standard structure.")
-
-
-@init_project.command("init-project")
-def cmd_init_project(
+def init_project(
     name: str = typer.Argument(..., help="Project name"),
     type: str = typer.Option("misc", help="Project type (code, homelab, automation, agent, research, misc)"),
     tags: str = typer.Option("", help="Comma-separated tags"),
@@ -86,11 +82,7 @@ def cmd_init_project(
 # =============================================================================
 # list command
 # =============================================================================
-list_projects = typer.Typer(help="List all projects.")
-
-
-@list_projects.command("list")
-def cmd_list_projects() -> None:
+def list_projects_cmd() -> None:
     """Show all projects with their status, last session, and next steps."""
     projects = list_projects()
 
@@ -125,11 +117,7 @@ def cmd_list_projects() -> None:
 # =============================================================================
 # show command
 # =============================================================================
-show_project = typer.Typer(help="Show project details.")
-
-
-@show_project.command("show")
-def cmd_show_project(slug: str = typer.Argument(..., help="Project slug")) -> None:
+def show_project(slug: str = typer.Argument(..., help="Project slug")) -> None:
     """Show detailed project information including status, context, last summary, blockers, and next steps."""
     # Load project
     project_dict = storage.read_project_meta(slug)
@@ -185,11 +173,7 @@ def cmd_show_project(slug: str = typer.Argument(..., help="Project slug")) -> No
 # =============================================================================
 # start command
 # =============================================================================
-start_session = typer.Typer(help="Start a work session.")
-
-
-@start_session.command("start")
-def cmd_start_session(
+def start_session(
     slug: str = typer.Argument(..., help="Project slug"),
     objective: Optional[str] = typer.Option(None, help="Session objective"),
 ) -> None:
@@ -248,11 +232,7 @@ def cmd_start_session(
 # =============================================================================
 # note command
 # =============================================================================
-add_note_cmd = typer.Typer(help="Add a note to the active session.")
-
-
-@add_note_cmd.command("note")
-def cmd_add_note(
+def add_note_cmd(
     text: str = typer.Argument(..., help="Note text"),
     type: str = typer.Option("work", help="Note type (work, change, blocker, decision, idea, reference)"),
 ) -> None:
@@ -291,11 +271,7 @@ def cmd_add_note(
 # =============================================================================
 # stop command
 # =============================================================================
-stop_session = typer.Typer(help="Stop the current session.")
-
-
-@stop_session.command("stop")
-def cmd_stop_session(
+def stop_session(
     slug: str = typer.Argument(..., help="Project slug"),
     add_to_changelog: bool = typer.Option(False, "--changelog", help="Add session summary to CHANGELOG.md"),
 ) -> None:
@@ -386,11 +362,7 @@ def cmd_stop_session(
 # =============================================================================
 # change command
 # =============================================================================
-add_change = typer.Typer(help="Add a change entry to CHANGELOG.md.")
-
-
-@add_change.command("change")
-def cmd_add_change(
+def add_change(
     slug: str = typer.Argument(..., help="Project slug"),
     type: str = typer.Option("code", help="Change type (code, infra, config, docs, automation, decision)"),
     title: str = typer.Option(..., help="Change title"),
@@ -418,11 +390,7 @@ def cmd_add_change(
 # =============================================================================
 # next command
 # =============================================================================
-suggest_next = typer.Typer(help="Suggest next steps for a project.")
-
-
-@suggest_next.command("next")
-def cmd_suggest_next(slug: str = typer.Argument(..., help="Project slug")) -> None:
+def suggest_next(slug: str = typer.Argument(..., help="Project slug")) -> None:
     """Suggest next steps based on project history and heuristics.
 
     Uses simple rules:
@@ -487,11 +455,7 @@ def cmd_suggest_next(slug: str = typer.Argument(..., help="Project slug")) -> No
 # =============================================================================
 # review command
 # =============================================================================
-review = typer.Typer(help="Review all projects.")
-
-
-@review.command("review")
-def cmd_review() -> None:
+def review() -> None:
     """Show an overview of all projects.
 
     Displays:
@@ -698,7 +662,7 @@ def _update_readme_autogen(slug: str, session: Session) -> None:
 # Register all commands at module level for direct access
 __all__ = [
     "init_project",
-    "list_projects",
+    "list_projects_cmd",
     "show_project",
     "start_session",
     "add_note_cmd",