Feature/733 sync dependency graph + arch dependencies

[vishalramvelu]

Summary

Improves agentic / architecture sync behavior around architecture.json dependencies:
Dependency graph visibility - build_dep_graph_from_architecture now returns DepGraphFromArchitectureResult (graph + warnings) instead of a bare dict. Warnings cover:
Orphan dependency filenames (no matching module entry in architecture.json)
Partial sync: dependency resolves to a module not in the sync target set (edge still omitted from the scheduled subgraph)
agentic_sync prints these as yellow Warning: lines when not in --quiet mode.
Preserve arch dependencies unless the prompt defines them -
update_architecture_from_prompt updates dependencies only when the prompt carries dependency intent: present (including empty tag to clear) or a non-empty parsed dependency list. Reason- / interface-only prompts no longer wipe existing dependencies.

pdd update repo-wide mode (if in this PR)

• New flags: --all, --budget, --dry-run (plus existing repo options: --extensions, --directory, --base-branch, etc.).
• --dry-run: drift report and estimated cost range without LLM calls or writes.

Tests

uv run pytest tests/test_agentic_sync_runner.py tests/test_agentic_sync.py tests/test_architecture_sync.py -v

• test_agentic_sync_runner: graph builder cases (basic deps, missing file, language suffix targets, partial sync warning, self-dep, orphan warning).
• test_agentic_sync: integration with DepGraphFromArchitectureResult / partial-sync warnings where applicable.
• test_architecture_sync: deps preserved without ; cleared with empty ; related sync_all / sequence tests updated.

Manual Tests

PR1 — REPL / one-off script (from repo root, uv run python):
Create a temp architecture.json with:
one entry whose dependencies include a nonexistent filename → expect an orphan warning;
one entry depending on a module outside the target basename list → partial sync warning;
Call build_dep_graph_from_architecture(path, ["mod_a", "mod_b"]) (adjust names) and inspect result.graph and result.warnings.

Checklist

• CI / local pytest green for the suites above
• Relevant Prompts changed and submitted PR to PDD_CAP

Change #735

[gltanaka]

target 3/30

[Copilot]

Pull request overview

This PR enhances dependency-aware behavior in agentic/architecture sync by adding richer dependency-graph results (graph + warnings) and preventing unintended dependency wipes during architecture sync. It also expands repository-wide pdd update behavior with dry-run reporting, budget caps, and post-update regeneration steps.

Changes:

• Make build_dep_graph_from_architecture return a DepGraphFromArchitectureResult (graph + warnings) and surface orphan/partial-sync warnings in agentic_sync.
• Update update_architecture_from_prompt to only modify dependencies when explicit <pdd-dependency> intent is present (including empty tags to clear).
• Extend repo-wide pdd update with --all, --dry-run, --budget, dependency ordering, drift reporting, and post-update example/doc regeneration + autosubmit hooks.

Reviewed changes

Copilot reviewed 16 out of 18 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
pdd/agentic_sync_runner.py	Introduces DepGraphFromArchitectureResult and emits validation warnings while building the dependency subgraph.
pdd/agentic_sync.py	Prints graph-builder warnings in non-quiet runs and adapts to new return type.
pdd/architecture_sync.py	Preserves architecture dependencies unless <pdd-dependency> metadata is explicitly present.
pdd/update_main.py	Adds repo-wide dry-run drift reporting, budget caps, dependency ordering, and post-update regeneration/submission steps.
pdd/commands/modify.py	Adds pdd update flags --all, --budget, --dry-run and enforces mode-specific validation.
tests/test_agentic_sync_runner.py	Updates/extends coverage for graph builder warnings and new return type.
tests/test_agentic_sync.py	Updates mocks/assertions for DepGraphFromArchitectureResult integration.
tests/test_architecture_sync.py	Updates tests to validate dependency preservation/clearing semantics.
tests/test_update_main.py	Adds coverage for drift-report doc counting, .mdx exclusion, dry-run/budget behavior, dependency ordering, and post-update hooks.
tests/test_update_command.py	Adds CLI coverage for --all, --dry-run, and --budget option handling and validation.
tests/test_sync_code_main.py	Updates assertions for new create_missing_prompts behavior when scanning.
pdd/prompts/core_dump_requirements_LLM.prompt	Adds/updates prompt spec content for core dump requirements.
pdd/prompts/agentic_e2e_fix_orchestrator_python.prompt	Adds convergence guard requirements to the orchestrator prompt.
project_dependencies.csv	Adds a repo dependency summary CSV artifact.
examples/prompts_linter/project_dependencies.csv	Removes example dependency CSV.
examples/hello/project_dependencies.csv	Removes example dependency CSV.
context/agentic_sync_runner_example.py	Updates example usage for new dep-graph return type.

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[gltanaka]

Hey Vishal, nice work on this PR! The dep graph warnings (Area 1) and the dependency preservation fix (Area 2) are solid — those are real bugs you've identified and the fixes are clean. The pdd update --all with dry-run and dependency ordering is a useful addition too. Tests look thorough.

A few things to clean up before we merge:

1. Remove uv.lock (+3,637 lines) — The repo doesn't currently use uv, so adding a lock file here is a big infrastructure decision that affects all contributors. Let's handle that separately if we decide to adopt uv.

2. Remove project_dependencies.csv (+258 lines) — This is an auto-generated artifact that will go stale and cause merge conflicts as soon as anyone else merges. Either remove it from the PR or add it to .gitignore.

3. _estimate_dry_run_cost_range unused params — I see ctx, repo_obj, and simple are still in the signature even though you mentioned dropping them in your reply to the Copilot review. Looks like the fix didn't make it into a commit — just need to clean those up.

Everything else looks good. These are quick fixes — looking forward to merging this once they're in!

[gltanaka]

Updating my earlier review — I was wrong about project_dependencies.csv, that's a legitimate PDD auto-deps artifact. Ignore that point. Apologies for the noise!

Revised asks (just two):

1. Remove uv.lock (+3,637 lines) — The repo doesn't currently use uv, so adding a lock file here is a big infrastructure decision that affects all contributors. Let's handle that separately if we decide to adopt uv.

2. _estimate_dry_run_cost_range unused params — I see ctx, repo_obj, and simple are still in the signature even though you mentioned dropping them in your reply to the Copilot review. Looks like the fix didn't make it into a commit — just need to clean those up.

Everything else looks good — the dep graph warnings, dep preservation fix, and pdd update --all features are solid work. Quick fixes and we can merge!