Design: one file for the agent, one for the CLI, and flags between them

Derived from requirements.md. Decisions recorded as decision-123.

The shape

One sentence: delete the reader, and give each of its eight keys a home that is not the repository. The CLI had one module that opened the harness config (harness_config.py, decision-044) and eight call sites that consumed what it read. Every call site is rewired to one of three sources — the CLI config, a constant, or a flag the agent passes — and the module is removed so the rule cannot regress quietly.

flowchart LR
  subgraph sources["sources after issue-352"]
    CC["cli-config.yaml<br/>routing.graph.specDir · critics[] · routing.graph.hooks"]
    K["constants<br/>PHASE_LABEL_PREFIX = loop:<br/>DEFAULT_SPEC_DIR = docs/specs"]
    F["flags the agent passes<br/>--spec-dir · --glob · --doc/--on-missing"]
    W["the work item<br/>ref → origin repo · loop → guestLoop"]
  end
  subgraph consumers["consumers"]
    B["graph/bootstrap.build_runtime"]
    G["graphlink (daemon coupling)"]
    V["core/graphs verbs + commands"]
    R["core/repo: scenarios · instructions · critics"]
    X["graph/extensions.read_declaration"]
  end
  CC --> B & R & X
  K --> B & G
  F --> V & R
  W --> G & B
  X --> B

Design points

#	Point	Where
D1	harness_config.py and harness-config.default.yaml deleted; graphlink.adopt/_adopt/_write_default and the dispatcher's two adopt calls removed; scaffold has no successor.	cli/the_loop/, graphlink.py, webhook/dispatcher.py
D2	bootstrap.resolve_spec_root(cli_cfg, override) is the one resolution: override → routing.graph.specDir → DEFAULT_SPEC_DIR. build_runtime and core.graphs._runtime call it; GraphLinkConfig.spec_dir empty means the default. --spec-dir rides check/graph → core.graphs.* → API bodies (specDir) → SDK Graph.*.	graph/bootstrap.py, core/graphs.py, commands/graph_cmd.py, api/routes.py, sdk/client.py
D3	PHASE_LABEL_PREFIX = "loop:" in graph/hooks/sideeffects.py; set-phase-label reads no config.	graph/hooks/sideeffects.py
D4	ghhost.origin_repo(root) (the slug parser moved from graphlink) supplies the in-session origin; build_runtime(origin_repo=…) takes the daemon's word first. graphlink._build_runtime passes f"{owner}/{repo}".	ghhost.py, graph/bootstrap.py, graphlink.py
D5	config["guestLoop"] = loop in GUEST_LOOPS replaces repoInitialized; Runtime.start and publish-artifact key on it.	graph/bootstrap.py, graph/runtime.py, graph/hooks/sideeffects.py
D6	_recipients reads ctx.params["roles"] only.	graph/hooks/sideeffects.py
D7	critics.load_critics(config_path=None) reads the resolved CLI config with _load_cli_config_raw(strict=True): absent → [], unparseable → CriticConfigError. core.repo.critics() ignores repo; critic_run finds by name.	critics.py, core/repo.py, commands/critic_cmd.py
D8	read_declaration(cli_config) parses routing.graph.hooks; load_graph(…, declaration=) replaces allow_repo_hooks; build_runtime parses once and applies to every runtime; graph hooks reports from load_cli_config_best_effort().	graph/extensions.py, graph/model.py, graph/bootstrap.py, commands/graph_cmd.py
D9	core.repo.scenarios(globs) → defaults when empty; core.repo.instructions(repo, docs, on_missing) builds the mapping instructions.collect_docs already reads; the command parses --doc (path or JSON object) and --on-missing; the API route and SDK/MCP gain the parameters.	core/repo.py, commands/instructions_cmd.py, commands/scenarios.py, api/routes.py, api/mcp.py, sdk/client.py
D10	Schemas: harness schema loses nine keys in the first pass and nine policy blocks in the second (autonomy, security, tdd, minimalism, tokenEconomy, selfImprovement, contextManagement, userInteraction, externalTools; the $defs only they used go with them) and rewrites its onboarding groups (people keeps no key — it establishes collaborators.yaml; automation is gone); CLI schema gains critics (the old items, minus object examples the runtime validator cannot walk, timeoutSeconds.minimum: 1) and routing.graph.hooks, loses repoHooks, defaults specDir to docs/specs; cli/the_loop/schemas/ copies follow. migrations.CURRENT_CONFIG_VERSION = "0.9.0"; _retire_repo_hooks pops the key and notes where critics and hooks live.	.the-loop/*.schema.json, cli/the_loop/schemas/, migrations.py
D11	Configs/templates: harness 0.3.0 without the removed blocks (eleven top-level keys remain: version, repository, workflow, tooling, customInstructions, testing, apiSpecs, design, hooks, observability, reviews); CLI 0.9.0 with critics: [] and routing.graph.{specDir, hooks} commented; validate_config.py drops the packaged-default target; hooks.json and rules/the-loop.mdc both test for harness-config.yaml.	.the-loop/, skills/the-loop/templates/, scripts/, hooks/, rules/
D12	Skill and commands: SKILL.md § Configuration rewritten with the key → flag table and the surviving key list; security.md, token-economy.md, context.md, minimalism.md state their rules directly instead of as config keys (the second review); test_writing_parity names the writing skill as a constant instead of reading userInteraction.writingStyle.skill; reviewing.md, automation.md, collaboration.md, workflow.md, tooling.md, instructions.md, testing.md; init.md step 4 from the graph, upgrade-the-loop.md migration block, <phaseLabelPrefix> → loop: everywhere.	skills/, commands/
D14	The third review: repository, tooling, hooks, observability leave the harness schema (six keys remain, required: [version]; onboarding groups instructions, workflow, testing, people, contracts-design); reviews becomes the CLI schema's top-level reviews (four defaulted keys). critics.load_review_policy(config_path) reads it the way load_critics does (absent → defaults, malformed → CriticConfigError); core.repo.review_policy(), the-loop critic policy [--format json], GET /repo/critics/policy (repoReviewPolicy, in the authored contract), Repo.review_policy (SDK, MCP). /init proposes only the six keys' values; reference/tooling.md's detection is the agent's per-session procedure.	critics.py, core/repo.py, commands/critic_cmd.py, api/routes.py, api/mcp.py, sdk/client.py, docs/api-specs/openapi/the-loop.v1.yaml, schemas, commands/init.md
D15	The fourth review: workflow leaves the harness schema (five keys remain; onboarding groups instructions, testing, people, contracts-design). The doc trees are the loop's convention — docs/specs/<id>/, docs/capabilities/, docs/learnings/ — written as literal paths in the skill, commands and docs; routing.graph.specDir's description says the convention and when to depart from it; /init scaffolds the fixed trees; upgrade-the-loop moves a differently placed tree with the operator's confirmation or reports it.	schemas, configs, commands/init.md, commands/upgrade-the-loop.md, skills/, docs/
D13	Docs: docs/config/harness-config.md rewritten around "what moved where"; critics-options.md new; routing-options.md graph.hooks.* + graph.specDir; command pages; capabilities with history rows; decision-123 supersedes decision-044.	docs/

Security design

• No read, no injection surface. A1–A3 of the requirements are closed by D1: there is no parser to reach with a crafted value.
• Executable configuration in the operator's file only. D7/D8 move both blocks; the CLI config joins this repository's sensitivePaths. The critics schema keeps env a string map and says "never a secret".
• Ownership proof unchanged. _checkout_belongs_to still gates the daemon's coupling on the origin remote (A4); _is_contained still bounds the operator's specDir (A3).
• --doc JSON is a selector of two fields. collect_docs reads path and notes; a doc's body never reaches the report (issue-132's boundary, unchanged).

Testing strategy

The testing plan is testing-plan.md. The centre of gravity is the negatives: a committed critic is inert, an undeclared hook module is never imported, a checkout's workflow.specDir is not consulted, and no verb writes into .the-loop/.