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/main.py

@@ -4,7 +4,7 @@ import typer
 
 from tracker.cli.commands import (
     init_project,
-    list_projects,
+    list_projects_cmd,
     show_project,
     start_session,
     add_note_cmd,
@@ -20,16 +20,16 @@ app = typer.Typer(
 )
 
 
-# Register all subcommands
-app.add_typer_command(init_project, name="init-project")
-app.add_typer_command(list_projects, name="list")
-app.add_typer_command(show_project, name="show")
-app.add_typer_command(start_session, name="start")
-app.add_typer_command(add_note_cmd, name="note")
-app.add_typer_command(stop_session, name="stop")
-app.add_typer_command(add_change, name="change")
-app.add_typer_command(suggest_next, name="next")
-app.add_typer_command(review, name="review")
+# Register all commands
+app.command("init-project")(init_project)
+app.command("list")(list_projects_cmd)
+app.command("show")(show_project)
+app.command("start")(start_session)
+app.command("note")(add_note_cmd)
+app.command("stop")(stop_session)
+app.command("change")(add_change)
+app.command("next")(suggest_next)
+app.command("review")(review)
 
 
 @app.callback()