feat: three-tier skill visibility, subset access control, and overrides

[Trecek]

Summary

Introduces a three-tier skill visibility system backed by a new skills_extended/ directory and config-driven subset categories, with enforcement at MCP server startup, kitchen open, and ephemeral skill dir construction. Reclassifies all 39 MCP tool tags into kitchen/headless/free-range tiers with category tags, and wires disabled subsets to block both tools and skills from sessions. Adds project-local skill override detection, recipe validation rules for disabled subsets and overrides, a cook-time interactive gate, and comprehensive documentation across four new docs files.

Individual Group Plans

Group A: MCP Tool Tag Reclassification

Reclassify the tag taxonomy for all 39 MCP tools: rename "automation" → "autoskillit" on every tool, move 11 formerly-ungated tools into the "kitchen" tier, introduce a new "headless" tag for test_check, remove the headless-session gate pre-open from _factory.py and server/__init__.py, and update the GATED_TOOLS / UNGATED_TOOLS / WORKER_TOOLS / HEADLESS_BLOCKED_UNGATED_TOOLS constants in core/types.py to match the new three-tier model. Apply functional category tags (github, ci, clone, telemetry) to all relevant tools.

Group B (Part A): Three-Tier Skill Directory Layout — Foundation

Creates the filesystem foundation for the three-tier skill visibility system: skills/ retains only open-kitchen, close-kitchen, sous-chef (3 dirs, Tier 1). New skills_extended/ holds the remaining 57 skills. SkillsConfig dataclass added to AutomationConfig with tier1/tier2/tier3 fields. defaults.yaml records canonical default tier assignments for all 60 skills.

Group B (Part B): Three-Tier Skill Directory Layout — Wiring

Wires the foundations into session distribution: removes hardcoded TIER2_SKILLS constant from session_skills.py, makes init_session() accept and use an AutomationConfig for tier-driven gating and unknown-skill warnings, adds --plugin-dir <pkg_root()> to chefs-hat, defaults run_skill's add_dir to bundled_skills_extended_dir().

Group C: Skill Category Metadata + Subset Config Schema

Add categories: frontmatter to 37 applicable bundled SKILL.md files, introduce a SubsetsConfig dataclass that extends AutomationConfig with subsets.disabled and subsets.custom_tags config keys, and add a read_skill_categories() helper to workspace/skills.py that exposes category membership on SkillInfo objects.

Group D: Subset Visibility Enforcement

Wire the config-driven subset category system into three runtime enforcement paths: (1) server startup mcp.disable(tags={subset}) in _initialize(), (2) open_kitchen re-disable loop after ctx.enable_components(tags={"kitchen"}) to neutralize FastMCP session-rule-overrides-server-rule behavior, and (3) ephemeral skill directory subset filter in init_session().

Group E: Project-Local Skill Overrides

Implement project-local skill override detection: when .claude/skills/<name>/SKILL.md or .autoskillit/skills/<name>/SKILL.md exists, the corresponding bundled skill is excluded from the ephemeral session directory. run_headless_core gains multi-path --add-dir support. A new WARNING recipe validation rule fires when a recipe references /autoskillit:<name> but a project-local override exists.

Group F: Recipe Validation for Disabled Subsets + Cook Gate

Extend recipe validation with subset-disabled-skill and subset-disabled-tool WARNING rules, add disabled_subsets field to ValidationContext, add TOOL_SUBSET_TAGS static map to core/types.py, and add a cook-time interactive prompt when disabled-subset findings are present.

Group G: Documentation

Write all user-facing documentation: four new files (docs/skill-visibility.md, docs/subset-categories.md, docs/mcp-tool-access.md, docs/project-local-overrides.md), and targeted updates to CLAUDE.md, docs/architecture.md, and docs/configuration.md.

Requirements

Tier System (TIER)

• REQ-TIER-001: Skills in skills/ (Tier 1) must be discoverable via --plugin-dir by Claude Code's native plugin scanner.
• REQ-TIER-002: Skills in skills_extended/ (Tier 2+3) must NOT be discoverable via --plugin-dir.
• REQ-TIER-003: autoskillit chefs-hat must copy skills from BOTH skills/ and skills_extended/ into the ephemeral session dir.
• REQ-TIER-004: run_headless_core must pass --add-dir pointing to skills_extended/ so headless sessions discover Tier 2+3 skills.
• REQ-TIER-005: SkillResolver must scan both skills/ and skills_extended/ directories for resolution and listing.
• REQ-TIER-006: Each skill must have a default tier assignment in package defaults.
• REQ-TIER-007: The config schema must support skills.tier1, skills.tier2, skills.tier3 keys for reclassification.
• REQ-TIER-008: Config-driven reclassification must be resolved at init_session() time using dynaconf layered resolution.
• REQ-TIER-009: A skill in multiple tier lists must produce a validation error at startup.
• REQ-TIER-010: Unrecognized skill names in tier config must produce a logged warning, not a crash.
• REQ-TIER-011: autoskillit chefs-hat must pass --plugin-dir <pkg_root()> to ensure MCP server loads without requiring autoskillit init.

MCP Tool Access (TOOL)

• REQ-TOOL-001 / REQ-TOOL-002: "headless" tag added; headless sessions pre-enable only headless-tagged tools (test_check), not full kitchen.
• REQ-TOOL-003 / REQ-TOOL-004: open_kitchen reveals all kitchen tools, then re-disables subset-tagged tools per config.
• REQ-TOOL-006: test_check reclassified as headless-accessible: {"autoskillit", "kitchen", "headless"}.
• REQ-TOOL-008: gate.enable() removed from _factory.py for headless sessions.
• REQ-TOOL-009 / REQ-TOOL-010: 11 formerly ungated tools gain "kitchen" tag; all 39 tools renamed "automation" → "autoskillit".

Category + Config + Visibility

• REQ-CAT-001..005: CATEGORY_TAGS registry, SKILL.md categories: frontmatter, subsets.custom_tags config support.
• REQ-CFG-001..005: subsets.disabled key, dynaconf resolution, graceful unknown-name handling.
• REQ-VIS-001..008: Tool hiding at startup, skill exclusion from sessions, open_kitchen re-disable loop.

Project-Local Overrides + Recipe Validation + Documentation

• REQ-OVR-001..004: Project-local overrides shadow bundled; multi-path --add-dir; recipe validation WARNING.
• REQ-VAL-001..004: subset-disabled-skill/tool rules; cook-time gate (interactive prompt / hard error).
• REQ-DOC-001..008: Four new docs files; CLAUDE.md, architecture.md, configuration.md updates.

Architecture Impact

Module Dependency Diagram

%%{init: {'flowchart': {'nodeSpacing': 50, 'rankSpacing': 70, 'curve': 'basis'}}}%%
graph TB
    %% CLASS DEFINITIONS %%
    classDef cli fill:#1a237e,stroke:#7986cb,stroke-width:2px,color:#fff;
    classDef stateNode fill:#004d40,stroke:#4db6ac,stroke-width:2px,color:#fff;
    classDef handler fill:#e65100,stroke:#ffb74d,stroke-width:2px,color:#fff;
    classDef phase fill:#6a1b9a,stroke:#ba68c8,stroke-width:2px,color:#fff;
    classDef newComponent fill:#2e7d32,stroke:#81c784,stroke-width:2px,color:#fff;
    classDef output fill:#00695c,stroke:#4db6ac,stroke-width:2px,color:#fff;
    classDef detector fill:#b71c1c,stroke:#ef5350,stroke-width:2px,color:#fff;
    classDef integration fill:#c62828,stroke:#ef9a9a,stroke-width:2px,color:#fff;

    subgraph L0 ["L0 — core/ (stdlib only)"]
        direction LR
        TYPES["● core/types.py<br/>━━━━━━━━━━<br/>★ HEADLESS_TOOLS<br/>★ FREE_RANGE_TOOLS<br/>★ CATEGORY_TAGS<br/>★ TOOL_SUBSET_TAGS<br/>● GATED_TOOLS, UNGATED_TOOLS"]
    end

    subgraph L1cfg ["L1 — config/"]
        direction LR
        SETTINGS["● config/settings.py<br/>━━━━━━━━━━<br/>★ SkillsConfig<br/>★ SubsetsConfig<br/>● AutomationConfig"]
    end

    subgraph L1pipe ["L1 — pipeline/"]
        direction LR
        GATE["● pipeline/gate.py<br/>━━━━━━━━━━<br/>● GATED_TOOLS<br/>● UNGATED_TOOLS<br/>(= FREE_RANGE_TOOLS)"]
    end

    subgraph L1ws ["L1 — workspace/"]
        direction LR
        SKILLS["● workspace/skills.py<br/>━━━━━━━━━━<br/>★ bundled_skills_extended_dir()<br/>★ read_skill_categories()<br/>★ detect_project_local_overrides()<br/>● SkillInfo.categories"]
        SESSK["● workspace/session_skills.py<br/>━━━━━━━━━━<br/>● init_session(config=, project_dir=)<br/>● subset filter via config.subsets<br/>● override detection"]
    end

    subgraph L1exec ["L1 — execution/"]
        direction LR
        HEADLESS["● execution/headless.py<br/>━━━━━━━━━━<br/>● add_dir → add_dirs: Sequence[str]<br/>● multi-path --add-dir support"]
    end

    subgraph L2 ["L2 — recipe/"]
        direction LR
        RULES_SK["● recipe/rules_skills.py<br/>━━━━━━━━━━<br/>★ subset-disabled-skill rule<br/>★ project-local-override rule"]
        RULES_T["● recipe/rules_tools.py<br/>━━━━━━━━━━<br/>★ subset-disabled-tool rule<br/>uses HEADLESS_TOOLS<br/>uses TOOL_SUBSET_TAGS"]
        ANALYSIS["● recipe/_analysis.py<br/>━━━━━━━━━━<br/>★ disabled_subsets field<br/>on ValidationContext"]
    end

    subgraph L3srv ["L3 — server/"]
        direction LR
        SRV_INIT["● server/__init__.py<br/>━━━━━━━━━━<br/>● mcp.disable(tags=subset)<br/>per config.subsets.disabled"]
        SRV_STATE["● server/_state.py<br/>━━━━━━━━━━<br/>calls _initialize(ctx)<br/>→ subset disable loop"]
        KITCHEN["● server/tools_kitchen.py<br/>━━━━━━━━━━<br/>★ re-disable subsets<br/>after open_kitchen<br/>session rule override fix"]
        FACTORY["● server/_factory.py<br/>━━━━━━━━━━<br/>● remove gate.enable()<br/>in headless sessions"]
        TOOLS_EXEC["● server/tools_execution.py<br/>━━━━━━━━━━<br/>● add_dir → add_dirs<br/>[skills_ext, cwd]"]
    end

    subgraph L3cli ["L3 — cli/"]
        direction LR
        CHEFSHAT["● cli/_chefs_hat.py<br/>━━━━━━━━━━<br/>★ --plugin-dir pkg_root()<br/>★ bundled_skills_extended_dir()<br/>● init_session(config=)"]
        APP["● cli/app.py<br/>━━━━━━━━━━<br/>★ cook-time subset gate<br/>★ disabled_subsets prompt<br/>interactive/non-interactive"]
    end

    subgraph L1ws_ext ["L1 — skills_extended/ (★ new dir)"]
        direction LR
        SKILLSEXT["★ skills_extended/<br/>━━━━━━━━━━<br/>57 SKILL.md files<br/>★ categories: frontmatter<br/>Tier 2+3 (NOT plugin-scanned)"]
    end

    %% VALID DEPENDENCIES — L0 exported to L1 %%
    SETTINGS -->|"imports CATEGORY_TAGS"| TYPES
    GATE -->|"imports GATED_TOOLS<br/>UNGATED_TOOLS"| TYPES
    SKILLS -->|"imports SkillSource<br/>load_yaml, pkg_root"| TYPES
    HEADLESS -->|"imports core.*"| TYPES

    %% L1 → L1 (intra-layer) %%
    SESSK -->|"imports SkillInfo<br/>SkillResolver<br/>detect_project_local_overrides"| SKILLS

    %% L2 → L1 %%
    RULES_T -->|"imports HEADLESS_TOOLS<br/>TOOL_SUBSET_TAGS"| TYPES
    RULES_SK -->|"imports workspace.*"| SKILLS
    ANALYSIS -->|"disabled_subsets field<br/>plumbed from config"| SETTINGS

    %% L3 → L2 %%
    SRV_STATE -->|"uses ToolContext"| GATE
    APP -->|"imports recipe.*<br/>make_validation_context"| ANALYSIS

    %% L3 → L1 %%
    SRV_STATE -->|"imports AutomationConfig"| SETTINGS
    CHEFSHAT -->|"imports bundled_skills_extended_dir<br/>SkillResolver"| SKILLS
    CHEFSHAT -->|"imports load_config"| SETTINGS
    TOOLS_EXEC -->|"passes add_dirs"| HEADLESS

    %% L3 → L3 (intra-layer) %%
    SRV_STATE -->|"_initialize(ctx)"| SRV_INIT
    KITCHEN -->|"calls ctx.disable_components<br/>after enable(kitchen)"| SRV_INIT
    FACTORY -->|"removes gate.enable()<br/>headless sessions"| GATE

    %% skills_extended consumed by %%
    SKILLSEXT -.->|"scanned by"| SKILLS
    SKILLS -->|"reads SKILL.md<br/>categories: frontmatter"| SKILLSEXT

    %% CLASS ASSIGNMENTS %%
    class TYPES stateNode;
    class SETTINGS,GATE handler;
    class SKILLS,SESSK,HEADLESS phase;
    class RULES_SK,RULES_T,ANALYSIS detector;
    class SRV_INIT,SRV_STATE,KITCHEN,FACTORY,TOOLS_EXEC cli;
    class CHEFSHAT,APP cli;
    class SKILLSEXT newComponent;

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Security Diagram

%%{init: {'flowchart': {'nodeSpacing': 44, 'rankSpacing': 56, 'curve': 'basis'}}}%%
flowchart TB
    %% CLASS DEFINITIONS %%
    classDef cli fill:#1a237e,stroke:#7986cb,stroke-width:2px,color:#fff;
    classDef stateNode fill:#004d40,stroke:#4db6ac,stroke-width:2px,color:#fff;
    classDef handler fill:#e65100,stroke:#ffb74d,stroke-width:2px,color:#fff;
    classDef phase fill:#6a1b9a,stroke:#ba68c8,stroke-width:2px,color:#fff;
    classDef newComponent fill:#2e7d32,stroke:#81c784,stroke-width:2px,color:#fff;
    classDef detector fill:#b71c1c,stroke:#ef5350,stroke-width:2px,color:#fff;
    classDef output fill:#00695c,stroke:#4db6ac,stroke-width:2px,color:#fff;
    classDef gap fill:#ff6f00,stroke:#ffa726,stroke-width:2px,color:#000;

    subgraph MCPBoundary ["MCP TOOL VISIBILITY BOUNDARY — server/__init__.py + _state.py"]
        direction TB
        FR["Free Range (2)<br/>━━━━━━━━━━<br/>open_kitchen<br/>close_kitchen<br/>tags: autoskillit only"]
        KIT_HIDE["● mcp.disable(tags='kitchen')<br/>━━━━━━━━━━<br/>36 kitchen + 1 headless<br/>hidden at module load"]
        SUB_HIDE["★ mcp.disable(tags=subset)<br/>━━━━━━━━━━<br/>per config.subsets.disabled<br/>e.g. github, ci, clone<br/>applied in _initialize()"]
        HL_REVEAL["● mcp.enable(tags='headless')<br/>━━━━━━━━━━<br/>AUTOSKILLIT_HEADLESS=1<br/>reveals test_check only<br/>★ HEADLESS_TOOLS constant"]
    end

    subgraph KitchenBoundary ["KITCHEN OPEN BOUNDARY — server/tools_kitchen.py"]
        direction TB
        OK_ENABLE["ctx.enable_components(tags='kitchen')<br/>━━━━━━━━━━<br/>Session rule: reveals 37 tools<br/>(overrides server-level!)"]
        REDISABLE["★ for subset in config.subsets.disabled:<br/>ctx.disable_components(tags=subset)<br/>━━━━━━━━━━<br/>Session rule after enable<br/>Later rule wins — re-hides subset tools<br/>Neutralizes FastMCP override behavior"]
        GUARD_HOOK["open_kitchen_guard.py<br/>━━━━━━━━━━<br/>PreToolUse hook (defense-in-depth)<br/>blocks open_kitchen from headless"]
    end

    subgraph HeadlessBoundary ["HEADLESS SESSION BOUNDARY — pipeline/gate.py + hooks/"]
        direction TB
        HL_GUARD["headless_orchestration_guard.py<br/>━━━━━━━━━━<br/>PreToolUse hook: blocks<br/>run_skill, run_cmd, run_python<br/>from headless sessions"]
        GATE_CHECK["● _require_not_headless()<br/>━━━━━━━━━━<br/>Code guard: orchestration triad<br/>defense-in-depth layer 2"]
        FACTORY_FIX["● server/_factory.py<br/>━━━━━━━━━━<br/>★ gate.enable() REMOVED<br/>headless sessions no longer<br/>pre-enable kitchen gate"]
    end

    subgraph SkillBoundary ["SKILL FILESYSTEM BOUNDARY — workspace/session_skills.py"]
        direction TB
        TIER1["skills/ — Tier 1<br/>━━━━━━━━━━<br/>Plugin-scanned by Claude Code<br/>open-kitchen, close-kitchen<br/>sous-chef (injected)"]
        T23["★ skills_extended/ — Tier 2+3<br/>━━━━━━━━━━<br/>NOT plugin-scanned<br/>57 skills with categories: frontmatter"]
        SUBSET_FILTER["★ init_session() subset filter<br/>━━━━━━━━━━<br/>Check SkillInfo.categories<br/>∩ config.subsets.disabled<br/>Skip if intersects → excluded"]
        OVR_FILTER["★ override detection<br/>━━━━━━━━━━<br/>detect_project_local_overrides()<br/>.claude/skills/ or<br/>.autoskillit/skills/ wins<br/>Bundled skill excluded"]
        EPH_DIR["Ephemeral skill dir<br/>━━━━━━━━━━<br/>subset-filtered<br/>override-aware copy<br/>passed via --add-dir"]
        TIER1 -->|"scanned at start"| SUBSET_FILTER
        T23 -->|"★ read categories:<br/>frontmatter"| SUBSET_FILTER
        SUBSET_FILTER -->|"disabled skills<br/>excluded"| OVR_FILTER
        OVR_FILTER -->|"bundled<br/>excluded if local exists"| EPH_DIR
    end

    subgraph RecipeBoundary ["RECIPE VALIDATION GATE — recipe/ + cli/app.py"]
        direction TB
        VAL_CTX["● make_validation_context()<br/>━━━━━━━━━━<br/>★ disabled_subsets=<br/>frozenset(cfg.subsets.disabled)"]
        SK_RULE["★ subset-disabled-skill rule<br/>━━━━━━━━━━<br/>recipe/rules_skills.py<br/>WARNING if skill.categories<br/>∩ disabled_subsets"]
        T_RULE["★ subset-disabled-tool rule<br/>━━━━━━━━━━<br/>recipe/rules_tools.py<br/>uses TOOL_SUBSET_TAGS<br/>WARNING if tool in disabled"]
        OVR_RULE["★ project-local-override rule<br/>━━━━━━━━━━<br/>recipe/rules_skills.py<br/>WARNING if /autoskillit:name<br/>has a project-local override"]
        COOK_GATE["★ cook-time subset gate<br/>━━━━━━━━━━<br/>cli/app.py cook()<br/>tty? → interactive prompt<br/>non-tty → hard error exit 1"]
        VAL_CTX --> SK_RULE
        VAL_CTX --> T_RULE
        VAL_CTX --> OVR_RULE
        SK_RULE --> COOK_GATE
        T_RULE --> COOK_GATE
        OVR_RULE --> COOK_GATE
    end

    %% TRUST FLOWS %%
    FR -->|"always visible"| KIT_HIDE
    KIT_HIDE -->|"37 kitchen tools<br/>hidden at startup"| SUB_HIDE
    SUB_HIDE -->|"subset tags additionally<br/>hidden per config"| HL_REVEAL
    OK_ENABLE -->|"session override attempt"| REDISABLE
    GUARD_HOOK -->|"blocks headless<br/>open_kitchen calls"| OK_ENABLE
    HL_GUARD -->|"hook layer"| GATE_CHECK
    GATE_CHECK -->|"code layer"| FACTORY_FIX

    %% CLASS ASSIGNMENTS %%
    class FR stateNode;
    class KIT_HIDE,SUB_HIDE,HL_REVEAL detector;
    class OK_ENABLE phase;
    class REDISABLE,GUARD_HOOK detector;
    class HL_GUARD,GATE_CHECK,FACTORY_FIX detector;
    class TIER1 output;
    class T23 newComponent;
    class SUBSET_FILTER,OVR_FILTER detector;
    class EPH_DIR output;
    class VAL_CTX handler;
    class SK_RULE,T_RULE,OVR_RULE detector;
    class COOK_GATE gap;

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State Lifecycle Diagram

%%{init: {'flowchart': {'nodeSpacing': 50, 'rankSpacing': 60, 'curve': 'basis'}}}%%
flowchart TB
    %% CLASS DEFINITIONS %%
    classDef cli fill:#1a237e,stroke:#7986cb,stroke-width:2px,color:#fff;
    classDef stateNode fill:#004d40,stroke:#4db6ac,stroke-width:2px,color:#fff;
    classDef handler fill:#e65100,stroke:#ffb74d,stroke-width:2px,color:#fff;
    classDef phase fill:#6a1b9a,stroke:#ba68c8,stroke-width:2px,color:#fff;
    classDef newComponent fill:#2e7d32,stroke:#81c784,stroke-width:2px,color:#fff;
    classDef detector fill:#b71c1c,stroke:#ef5350,stroke-width:2px,color:#fff;
    classDef output fill:#00695c,stroke:#4db6ac,stroke-width:2px,color:#fff;
    classDef gap fill:#ff6f00,stroke:#ffa726,stroke-width:2px,color:#000;

    subgraph L0const ["L0 CONSTANTS — core/types.py (INIT_ONLY: module load)"]
        direction LR
        HTCONST["★ HEADLESS_TOOLS<br/>━━━━━━━━━━<br/>frozenset({'test_check'})<br/>INIT_ONLY: module-level"]
        FRCONST["★ FREE_RANGE_TOOLS<br/>━━━━━━━━━━<br/>frozenset({open_kitchen,<br/>close_kitchen})<br/>INIT_ONLY: module-level"]
        CATTAGS["★ CATEGORY_TAGS<br/>━━━━━━━━━━<br/>frozenset{github,ci,clone,<br/>telemetry,arch-lens,audit}<br/>INIT_ONLY: module-level"]
        TOOLMAP["★ TOOL_SUBSET_TAGS<br/>━━━━━━━━━━<br/>dict[tool → frozenset[tag]]<br/>INIT_ONLY: module-level"]
    end

    subgraph L1cfg ["L1 CONFIG — config/settings.py (INIT_ONLY: from_dynaconf())"]
        direction TB
        SUBSETS["★ SubsetsConfig<br/>━━━━━━━━━━<br/>disabled: list[str]<br/>custom_tags: dict[str, list[str]]<br/>INIT_ONLY after construction<br/>⚠ warns on unknown names"]
        SKILLSCFG["★ SkillsConfig<br/>━━━━━━━━━━<br/>tier1: list[str]<br/>tier2: list[str]<br/>tier3: list[str]<br/>INIT_ONLY after construction<br/>⚠ raises on duplicates"]
        AUTOCFG["● AutomationConfig<br/>━━━━━━━━━━<br/>subsets: SubsetsConfig<br/>skills: SkillsConfig<br/>INIT_ONLY: frozen dataclass<br/>__post_init__ validates"]
        SUBCFG_VAL["● AutomationConfig.__post_init__<br/>━━━━━━━━━━<br/>validates: no duplicate tiers<br/>validates: known category names<br/>GATE: ValueError on duplicate<br/>GATE: warning on unknown name"]
        SUBSETS --> AUTOCFG
        SKILLSCFG --> AUTOCFG
        AUTOCFG --> SUBCFG_VAL
    end

    subgraph L1ws ["L1 WORKSPACE — workspace/skills.py (INIT_ONLY: scan time)"]
        direction TB
        SKILLINFO["● SkillInfo<br/>━━━━━━━━━━<br/>★ categories: frozenset[str]<br/>INIT_ONLY: set by _scan_directory()<br/>source: read_skill_categories(SKILL.md)"]
        RDCAT["★ read_skill_categories()<br/>━━━━━━━━━━<br/>Path → frozenset[str]<br/>Reads categories: from SKILL.md<br/>INIT_ONLY: once per scan<br/>empty set if absent/malformed"]
        RDCAT --> SKILLINFO
    end

    subgraph L1session ["L1 SESSION INIT — workspace/session_skills.py (MUTABLE: rebuilt each call)"]
        direction TB
        INIT_S["● init_session(config, project_dir)<br/>━━━━━━━━━━<br/>Reads: config.subsets.disabled<br/>Reads: config.skills.tier2<br/>Reads: detect_project_local_overrides()<br/>Reads: skill_info.categories"]
        SUB_CHECK["★ subset intersection check<br/>━━━━━━━━━━<br/>skill.categories ∩ disabled_subsets<br/>→ skip if non-empty<br/>GATE: per-skill filter"]
        OVR_CHECK["★ override check<br/>━━━━━━━━━━<br/>skill.name in local_overrides<br/>→ skip bundled if local exists<br/>GATE: per-skill filter"]
        EPH["Ephemeral skill dir<br/>━━━━━━━━━━<br/>MUTABLE: rebuilt each session<br/>Filtered copy of skills_extended/"]
        INIT_S --> SUB_CHECK
        SUB_CHECK --> OVR_CHECK
        OVR_CHECK --> EPH
    end

    subgraph L2val ["L2 RECIPE VALIDATION — recipe/ (DERIVED: per validation run)"]
        direction TB
        VALCTX["★ ValidationContext.disabled_subsets<br/>━━━━━━━━━━<br/>frozenset: DERIVED from config<br/>INIT_ONLY for validation run<br/>plumbed via make_validation_context()"]
        SK_RULE_STATE["★ subset-disabled-skill rule<br/>━━━━━━━━━━<br/>Reads: skill.categories<br/>Reads: ctx.disabled_subsets<br/>Emits: WARNING finding<br/>DERIVED: stateless rule"]
        T_RULE_STATE["★ subset-disabled-tool rule<br/>━━━━━━━━━━<br/>Reads: TOOL_SUBSET_TAGS[tool]<br/>Reads: ctx.disabled_subsets<br/>Emits: WARNING finding<br/>DERIVED: stateless rule"]
        VALCTX --> SK_RULE_STATE
        VALCTX --> T_RULE_STATE
    end

    %% GATES AND VALIDATION FLOWS %%
    CATTAGS -->|"validates against"| SUBCFG_VAL
    HTCONST -->|"HEADLESS_TOOLS<br/>used by rules_tools"| T_RULE_STATE
    TOOLMAP -->|"TOOL_SUBSET_TAGS<br/>used by rules_tools"| T_RULE_STATE
    SUBCFG_VAL -->|"subsets.disabled<br/>plumbed to"| VALCTX
    SUBCFG_VAL -->|"subsets.disabled<br/>used by"| INIT_S
    SKILLINFO -->|"categories<br/>read by subset check"| SUB_CHECK
    SKILLINFO -->|"categories<br/>read by skill rule"| SK_RULE_STATE

    %% CLASS ASSIGNMENTS %%
    class HTCONST,FRCONST,CATTAGS,TOOLMAP detector;
    class SUBSETS,SKILLSCFG newComponent;
    class AUTOCFG handler;
    class SUBCFG_VAL stateNode;
    class SKILLINFO phase;
    class RDCAT newComponent;
    class INIT_S handler;
    class SUB_CHECK,OVR_CHECK stateNode;
    class EPH output;
    class VALCTX newComponent;
    class SK_RULE_STATE,T_RULE_STATE detector;

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Closes #306

Implementation Plan

Plan files:

• /home/talon/projects/autoskillit-runs/impl-20260315-172637-050288/temp/make-plan/skill-tool-access-control-group-a_plan_2026-03-15_180000.md
• /home/talon/projects/autoskillit-runs/impl-20260315-172637-050288/temp/make-plan/groupB_skill_directory_layout_plan_2026-03-15_172700_part_a.md
• /home/talon/projects/autoskillit-runs/impl-20260315-172637-050288/temp/make-plan/groupB_skill_directory_layout_plan_2026-03-15_172700_part_b.md
• /home/talon/projects/autoskillit-runs/impl-20260315-172637-050288/temp/make-plan/groupC_skill_category_metadata_subset_config_plan_2026-03-15_202248_part_a.md
• /home/talon/projects/autoskillit-runs/impl-20260315-172637-050288/temp/make-plan/groupD_subset_visibility_enforcement_plan_2026-03-15_202800.md
• /home/talon/projects/autoskillit-runs/impl-20260315-172637-050288/temp/make-plan/groupE_project_local_overrides_plan_2026-03-15_172637_part_a.md
• /home/talon/projects/autoskillit-runs/impl-20260315-172637-050288/temp/make-plan/groupF_recipe_validation_subset_disabled_plan_2026-03-15_221419.md
• /home/talon/projects/autoskillit-runs/impl-20260315-172637-050288/temp/make-plan/groupG_documentation_plan_2026-03-15_172700.md

Token Usage Summary

No token usage data available for this pipeline run.

🤖 Generated with Claude Code via AutoSkillit

[Trecek]

AutoSkillit PR Review — Verdict: changes_requested (23 blocking issues found; 2 critical arch violations, 1 critical bug, 14 warnings, 6 decision items)

[Trecek]

[warning] arch: run_skill hardcodes add_dirs=[str(pkg_root() / 'skills_extended'), cwd], embedding session directory composition policy in the server layer. This policy belongs in the execution or workspace layer, not in the MCP tool handler.

[Trecek]

[warning] arch: run_skill hardcodes add_dirs=[str(pkg_root() / 'skills_extended'), cwd], embedding session directory composition policy in the server layer. This policy belongs in the execution or workspace layer, not in the MCP tool handler.

[Trecek]

[warning] bugs: test_check carries both 'kitchen' (disabled at startup) and 'headless' tags. Correctness depends entirely on FastMCP using OR semantics for tag-based visibility (any enabled tag makes tool visible). If FastMCP uses AND semantics, test_check remains invisible in headless sessions since 'kitchen' stays disabled. This assumption is undocumented and untested.

[Trecek]

AutoSkillit PR Review — Verdict: changes_requested. Found 21 actionable findings (2 additional critical findings at tests/server/test_server_init.py L1265 and L1280 are outside diff hunks and included in this summary only). See inline comments.

[Trecek]

[warning] arch: TOOL_SUBSET_TAGS in L0 (core/) encodes server-layer semantic knowledge: which MCP tools carry which functional-category FastMCP tags. The comment explicitly says it 'Mirrors the FastMCP @mcp.tool(tags=...) category assignments in the server layer.' This couples L0 to server-layer tagging decisions; any tag change in server/tools_*.py requires a corresponding update in L0. This data belongs in L1 (pipeline/) or L3 (server/) where it can reference both L0 constants and server-layer contracts.

[Trecek]

[warning] arch: Cross-L1 import: workspace/ (L1) imports AutomationConfig from config/settings.py (also L1) under TYPE_CHECKING. Per the architecture, L1 packages should only import from L0 (core/). Accept the config data as a protocol/TypedDict defined in core/, or use Any/string-quoted forward reference.

[Trecek]

[warning] slop: UNGATED_TOOLS is defined as a pure alias for FREE_RANGE_TOOLS (UNGATED_TOOLS: frozenset[str] = FREE_RANGE_TOOLS). This is a backward-compat shim — callers should import FREE_RANGE_TOOLS directly. WORKER_TOOLS and HEADLESS_BLOCKED_UNGATED_TOOLS were removed entirely while UNGATED_TOOLS was kept; apply consistent policy (either alias all removed names or remove all).

[Trecek]

AutoSkillit review found 21 actionable blocking issues. See inline review comments for details. Verdict: changes_requested.

[Trecek]

AutoSkillit review found 21 actionable blocking issues (plus 2 critical xdist-unsafe tests at test_server_init.py L1265/L1280 outside diff hunks). See inline review comments for details. Verdict: changes_requested.