refactor: master tracking issue — code review & simplify all modules

[thomaschristory]

Overview

Full codebase review + simplify pass. Each child issue is scoped to one module area. Work is organised in three waves based on dependency order — agents working on later waves must wait for earlier waves to stabilise.

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Coordination protocol (agents: read this)

Before starting any child issue:

1. Check this issue's comments — if another agent claimed the issue within the last 24 h and has not posted a blocker/handoff, stop and surface the conflict.
2. Post a claim comment on the child issue stating: what you are doing, which branch you are on, expected scope.
3. Post milestone updates on the child issue: branch pushed, PR opened, CI green.
4. Post a completion comment when merged or abandoned.

Keep comments to 1–3 lines. Do not spam.

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Wave 1 — leaf/core modules (fully parallel, no dependencies)

These are safe to run simultaneously. They do not depend on each other.

Issue	Scope	Lines
#58	nsc/schema/ parsing layer (models, loader, hashing)	~180
#59	Foundation layer: model/command_model.py, aliases/resolver.py, auth/verify.py	~380
#55	nsc/config/ package (writer, loader, models, settings)	~420
#57	nsc/output/ package (errors, explain, table, render, csv_)	~640
#50	nsc/http/ package (client, audit, retry, errors)	~750
#52	nsc/cache/store.py + nsc/schema/source.py	~584

Start Wave 2 only after all Wave 1 PRs are merged to main.

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Wave 2 — builder + CLI core (run after Wave 1)

These consume model/, output/, or http/ and must see the stabilised versions.

Issue	Scope	Lines
#49	nsc/builder/build.py	514
#51	nsc/cli/writes/ pipeline (input, bulk, preflight, apply, confirmation)	~1 044
#47	nsc/cli/handlers.py	660
#48	nsc/cli/registration.py	465

Start Wave 3 only after all Wave 2 PRs are merged to main.

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Wave 3 — CLI sub-commands (run after Wave 2)

These sit on top of handlers + registration and must see the stabilised CLI core.

Issue	Scope	Lines
#53	CLI entry-points: app.py, runtime.py, login_commands.py	~933
#54	CLI management commands: aliases, profiles, skill	~765
#56	CLI utility commands: config, cache, init	~420

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What each agent should do

1. Pick an unstarted issue in the current wave.
2. Run just lint and just test on the unmodified code first to establish a baseline.
3. Review the files listed in the issue for: dead branches, over-defensive conditionals, logic in the wrong layer, loose type annotations, and what-comments (remove them).
4. Simplify. Keep all behaviour identical. Do not add features.
5. Run just lint and just test again — both must be green before opening a PR.
6. Open a PR against main, squash-merge after CI passes.

[thomaschristory]

All waves complete.

[thomaschristory]

All 3 waves complete.
Wave 1 PRs: #61 #62 #63 #64 #65 #66
Wave 2 PRs: #68 #69 (issues #47 and #48 needed no changes)
Wave 3 PRs: #70 (issues #53 and #54 needed no changes)
All merged to main.