validate-arch-includes reports 153 warnings on current repo — needs cleanup plan

[gltanaka]

Problem

Running pdd validate-arch-includes on the current repo produces 153 warnings:

• Architecture entries referencing prompt files that don't exist on disk (e.g. candidate_models_Python.prompt, config_loader_Python.prompt)
• Prompts that <include> modules not listed in architecture.json dependencies (e.g. llm_invoke, load_prompt_template referenced by many modules)
• Architecture.json listing dependencies that prompts don't actually <include>

The CI workflow step (added in PR #757) emits a GitHub warning annotation on every PR. With 153 existing mismatches, this warning is permanently present and will be ignored.

Proposed fix

1. Triage the 153 warnings — which are stale architecture entries to remove vs missing deps to add
2. Fix the most common pattern (many modules include llm_invoke_example.py / load_prompt_template_example.py without corresponding architecture deps)
3. Once warnings are under control, consider making the CI step blocking

Context

Discovered during E2E validation of PR #757. The mismatches are pre-existing drift, not introduced by the PR.

[gltanaka]

Closing — the cleanup this issue asked for has been done.

State now vs. when filed:

• Warnings (default repo scope): 153 → 1
• CI step: warning annotation → blocking (.github/workflows/unit-tests.yml:60, plain run: with no continue-on-error)

What landed:

• d8a46d8c3 — "remove 18 orphaned entries and sync stale dependencies in architecture.json" (−1565 / +101 lines) did the bulk triage.
• The command moved from standalone pdd validate-arch-includes to pdd checkup --validate-arch-includes (see pdd/commands/checkup.py).
• Proposal item 3 ("consider making CI blocking") is already in effect — CI runs both a fixture smoke test and the full repo scan, both blocking.

Remaining drift (newly introduced by 82e03fb24 for #1143, unrelated to this issue):
architecture.json lists architecture_sync_python.prompt as a dependency of agentic_change_orchestrator_python.prompt, but the orchestrator prompt only <include>s context/architecture_sync_example.py — the validator requires the .prompt file itself. That's a one-line follow-up, not the large-scale drift this issue tracked.