refactor(storage): phase 3 normalize runtime storage roots

[Orinks]

Summary

Now that #467 / PR #468 moved alert + notification event persistence into the unified runtime store, the main remaining refactor work is broader path/root normalization.

Today the app still has multiple active ways of deciding where writable files live:

• ConfigManager anchors config under config_dir / app.paths.config
• Paths still exposes independent Data/Config/Cache/Logs roots
• some callers still bypass the runtime config root and pick paths directly

That means portable mode, --config-dir, and default installed layouts are not yet driven by one canonical runtime storage contract.

Phase 3 goal

Make all actively used writable surfaces resolve from one canonical runtime storage layout, with migration-safe behavior.

In scope

1) Define a single runtime storage contract

Touch:

• src/accessiweather/app.py
• src/accessiweather/app_initialization.py
• src/accessiweather/paths.py (or replacement helper if cleaner)
• src/accessiweather/config/config_manager.py

Expected result:

• app startup resolves storage roots once
• downstream code stops inferring its own roots ad hoc
• portable mode and explicit --config-dir are honored consistently

2) Move active callers onto that contract

Touch at least:

• src/accessiweather/app_initialization.py
  • stop deriving cache from config_dir fallback logic inline
• src/accessiweather/single_instance.py
  • ensure lock-file location follows the same runtime storage contract
• src/accessiweather/ui/dialogs/noaa_radio_dialog.py
• src/accessiweather/noaa_radio/preferences.py
  • stop creating prefs from a fresh Paths().data detached from runtime overrides

Also audit any still-active callers using app.paths.* directly for persistence so they either:

• intentionally use the canonical root, or
• are explicitly documented as legacy and deferred

3) Keep current runtime-state/file migration behavior intact

Do not rework the Phase 2 runtime-state schema.
Keep working behavior for:

• accessiweather.json
• state/runtime_state.json
• portable API-key bundles

Migration / safety constraints

• no destructive data moves unless there is a tested read-old/write-new path
• prefer “resolve canonically, then write there” over large one-shot migrations
• keep user-visible storage surprises to a minimum

Tests / validation

Add focused regression coverage for:

• installed/default layout
• portable layout
• explicit --config-dir
• NOAA radio prefs honoring the same runtime root
• single-instance lock honoring the same runtime root
• weather cache honoring the same runtime root

Out of scope

• deleting legacy helper modules outright
• mass renaming on-disk folders just for style
• changing config schema unrelated to storage-root normalization
• broad documentation sweeps beyond what is needed to explain the new contract

Follow-up

After this lands, do a short soak / observation pass before removing legacy path fallbacks.