Restructure backend into a single layered app/ package

As Discussed in #501.

What

Consolidates the two top-level Python folders (api/ FastAPI service + src/ LLM/PDF engine) into one importable app/ package with clear layers.

app/
  main.py          # create_app() factory + lifespan
  api/
    router.py      # aggregates all routers
    routes/        # forms.py, templates.py
    schemas/
    deps.py
  core/            # config, logging, lifespan, error handlers
  services/        # llm, file_manipulator, filler, controller (was src/)
  models/          # ORM models
  db/              # database, init_db, repositories

Changes

• All internal imports rewritten from api.* / src.* to app.*.
• Entry-point references updated to app.main:app (Dockerfile, docker-compose, Makefile, release workflow).
• Scattered os.getenv calls and runtime paths are centralized in app/core/config.py, and the old src/main.py demo now lives at examples/pipeline_demo.py.

Closes #513 .
Part of #512.