@zigrivers/scaffold 3.5.1 → 3.5.3

package/dist/cli/commands/complete.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"complete.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/complete.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,OAAO,CAAA;AAS1C,UAAU,YAAY;IACpB,IAAI,EAAE,MAAM,CAAA;IACZ,MAAM,CAAC,EAAE,MAAM,CAAA;IACf,IAAI,CAAC,EAAE,OAAO,CAAA;IACd,OAAO,CAAC,EAAE,OAAO,CAAA;IACjB,IAAI,CAAC,EAAE,MAAM,CAAA;IACb,KAAK,CAAC,EAAE,OAAO,CAAA;CAChB;AAED,QAAA,MAAM,eAAe,EAAE,aAAa,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAAE,YAAY,CAqGzE,CAAA;AAED,eAAe,eAAe,CAAA"}
+{"version":3,"file":"complete.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/complete.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,OAAO,CAAA;AAU1C,UAAU,YAAY;IACpB,IAAI,EAAE,MAAM,CAAA;IACZ,MAAM,CAAC,EAAE,MAAM,CAAA;IACf,IAAI,CAAC,EAAE,OAAO,CAAA;IACd,OAAO,CAAC,EAAE,OAAO,CAAA;IACjB,IAAI,CAAC,EAAE,MAAM,CAAA;IACb,KAAK,CAAC,EAAE,OAAO,CAAA;CAChB;AAED,QAAA,MAAM,eAAe,EAAE,aAAa,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAAE,YAAY,CAuGzE,CAAA;AAED,eAAe,eAAe,CAAA"}

package/dist/cli/commands/complete.js

@@ -4,7 +4,8 @@ import { createOutputContext } from '../output/context.js';
 import { StateManager } from '../../state/state-manager.js';
 import { acquireLock, releaseLock } from '../../state/lock-manager.js';
 import { findClosestMatch } from '../../utils/levenshtein.js';
-import { buildComputeEligibleFn } from '../../utils/eligible.js';
+import { loadPipelineContext } from '../../core/pipeline/context.js';
+import { resolvePipeline } from '../../core/pipeline/resolver.js';
 const completeCommand = {
     command: 'complete <step>',
     describe: 'Mark a step as completed (for steps executed outside scaffold run)',
@@ -37,7 +38,9 @@ const completeCommand = {
             return;
         }
         try {
-            const stateManager = new StateManager(projectRoot, buildComputeEligibleFn(projectRoot));
+            const context = loadPipelineContext(projectRoot);
+            const pipeline = resolvePipeline(context);
+            const stateManager = new StateManager(projectRoot, pipeline.computeEligible);
             const state = stateManager.loadState();
             // Check step exists in state
             if (!(argv.step in state.steps)) {

package/dist/cli/commands/complete.js.map

@@ -1 +1 @@
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+{"version":3,"file":"complete.js","sourceRoot":"","sources":["../../../src/cli/commands/complete.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,eAAe,EAAE,MAAM,+BAA+B,CAAA;AAC/D,OAAO,EAAE,iBAAiB,EAAE,MAAM,8BAA8B,CAAA;AAChE,OAAO,EAAE,mBAAmB,EAAE,MAAM,sBAAsB,CAAA;AAC1D,OAAO,EAAE,YAAY,EAAE,MAAM,8BAA8B,CAAA;AAC3D,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,MAAM,6BAA6B,CAAA;AACtE,OAAO,EAAE,gBAAgB,EAAE,MAAM,4BAA4B,CAAA;AAC7D,OAAO,EAAE,mBAAmB,EAAE,MAAM,gCAAgC,CAAA;AACpE,OAAO,EAAE,eAAe,EAAE,MAAM,iCAAiC,CAAA;AAWjE,MAAM,eAAe,GAAyD;IAC5E,OAAO,EAAE,iBAAiB;IAC1B,QAAQ,EAAE,oEAAoE;IAC9E,OAAO,EAAE,CAAC,KAAK,EAAE,EAAE;QACjB,OAAO,KAAK,CAAC,UAAU,CAAC,MAAM,EAAE;YAC9B,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,gCAAgC;YAC7C,YAAY,EAAE,IAAI;SACnB,CAAC,CAAA;IACJ,CAAC;IACD,OAAO,EAAE,KAAK,EAAE,IAAI,EAAE,EAAE;QACtB,MAAM,WAAW,GAAG,IAAI,CAAC,IAAI,IAAI,eAAe,CAAC,OAAO,CAAC,GAAG,EAAE,CAAC,CAAA;QAC/D,IAAI,CAAC,WAAW,EAAE,CAAC;YACjB,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,yEAAyE,CAAC,CAAA;YAC/F,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;YACf,OAAM;QACR,CAAC;QAED,MAAM,UAAU,GAAG,iBAAiB,CAAC,IAAI,CAAC,CAAA;QAC1C,MAAM,MAAM,GAAG,mBAAmB,CAAC,UAAU,CAAC,CAAA;QAE9C,eAAe;QACf,MAAM,UAAU,GAAG,WAAW,CAAC,WAAW,EAAE,UAAU,EAAE,IAAI,CAAC,IAAI,CAAC,CAAA;QAClE,IAAI,CAAC,UAAU,CAAC,QAAQ,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC;YACxC,IAAI,UAAU,CAAC,KAAK,EAAE,CAAC;gBACrB,MAAM,CAAC,IAAI,CAAC,GAAG,UAAU,CAAC,KAAK,CAAC,IAAI,KAAK,UAAU,CAAC,KAAK,CAAC,OAAO,EAAE,CAAC,CAAA;YACtE,CAAC;iBAAM,CAAC;gBACN,MAAM,CAAC,IAAI,CAAC,iCAAiC,CAAC,CAAA;YAChD,CAAC;YACD,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;YACf,OAAM;QACR,CAAC;QAED,IAAI,CAAC;YACH,MAAM,OAAO,GAAG,mBAAmB,CAAC,WAAW,CAAC,CAAA;YAChD,MAAM,QAAQ,GAAG,eAAe,CAAC,OAAO,CAAC,CAAA;YACzC,MAAM,YAAY,GAAG,IAAI,YAAY,CAAC,WAAW,EAAE,QAAQ,CAAC,eAAe,CAAC,CAAA;YAC5E,MAAM,KAAK,GAAG,YAAY,CAAC,SAAS,EAAE,CAAA;YAEtC,6BAA6B;YAC7B,IAAI,CAAC,CAAC,IAAI,CAAC,IAAI,IAAI,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC;gBAChC,MAAM,UAAU,GAAG,gBAAgB,CAAC,IAAI,CAAC,IAAI,EAAE,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAA;gBACxE,MAAM,GAAG,GAAG,UAAU;oBACpB,CAAC,CAAC,SAAS,IAAI,CAAC,IAAI,8BAA8B,UAAU,IAAI;oBAChE,CAAC,CAAC,SAAS,IAAI,CAAC,IAAI,aAAa,CAAA;gBACnC,MAAM,CAAC,KAAK,CAAC;oBACX,IAAI,EAAE,oBAAoB;oBAC1B,OAAO,EAAE,GAAG;oBACZ,QAAQ,EAAE,CAAC;oBACX,QAAQ,EAAE,4CAA4C;iBACvD,CAAC,CAAA;gBACF,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;gBACf,OAAM;YACR,CAAC;YAED,MAAM,SAAS,GAAG,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAExC,8CAA8C;YAC9C,IAAI,SAAS,CAAC,MAAM,KAAK,WAAW,EAAE,CAAC;gBACrC,IAAI,UAAU,KAAK,MAAM,EAAE,CAAC;oBAC1B,MAAM,CAAC,MAAM,CAAC,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,MAAM,EAAE,WAAW,EAAE,gBAAgB,EAAE,IAAI,EAAE,CAAC,CAAA;gBACjF,CAAC;qBAAM,CAAC;oBACN,MAAM,CAAC,IAAI,CAAC,SAAS,IAAI,CAAC,IAAI,wBAAwB,CAAC,CAAA;gBACzD,CAAC;gBACD,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;gBACf,OAAM;YACR,CAAC;YAED,MAAM,cAAc,GAAG,SAAS,CAAC,MAAM,CAAA;YAEvC,oBAAoB;YACpB,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG;gBACvB,MAAM,EAAE,WAAW;gBACnB,MAAM,EAAE,SAAS,CAAC,MAAM,IAAI,UAAU;gBACtC,QAAQ,EAAE,SAAS,CAAC,QAAQ,IAAI,EAAE;gBAClC,EAAE,EAAE,IAAI,IAAI,EAAE,CAAC,WAAW,EAAE;gBAC5B,YAAY,EAAE,MAAM;aACrB,CAAA;YAED,+CAA+C;YAC/C,IAAI,KAAK,CAAC,WAAW,EAAE,IAAI,KAAK,IAAI,CAAC,IAAI,EAAE,CAAC;gBAC1C,KAAK,CAAC,WAAW,GAAG,IAAI,CAAA;YAC1B,CAAC;YAED,YAAY,CAAC,SAAS,CAAC,KAAK,CAAC,CAAA;YAE7B,IAAI,UAAU,KAAK,MAAM,EAAE,CAAC;gBAC1B,MAAM,CAAC,MAAM,CAAC;oBACZ,IAAI,EAAE,IAAI,CAAC,IAAI;oBACf,cAAc;oBACd,SAAS,EAAE,WAAW;iBACvB,CAAC,CAAA;YACJ,CAAC;iBAAM,CAAC;gBACN,MAAM,CAAC,OAAO,CAAC,SAAS,IAAI,CAAC,IAAI,8BAA8B,cAAc,GAAG,CAAC,CAAA;gBACjF,MAAM,CAAC,IAAI,CAAC,2CAA2C,CAAC,CAAA;YAC1D,CAAC;YACD,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACjB,CAAC;gBAAS,CAAC;YACT,IAAI,UAAU,CAAC,QAAQ,EAAE,CAAC;gBACxB,WAAW,CAAC,WAAW,CAAC,CAAA;YAC1B,CAAC;QACH,CAAC;IACH,CAAC;CACF,CAAA;AAED,eAAe,eAAe,CAAA"}

package/dist/cli/commands/next.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"next.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/next.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,OAAO,CAAA;AAc1C,UAAU,QAAQ;IAChB,KAAK,CAAC,EAAE,MAAM,CAAA;IACd,MAAM,CAAC,EAAE,MAAM,CAAA;IACf,IAAI,CAAC,EAAE,OAAO,CAAA;IACd,OAAO,CAAC,EAAE,OAAO,CAAA;IACjB,IAAI,CAAC,EAAE,MAAM,CAAA;IACb,KAAK,CAAC,EAAE,OAAO,CAAA;CAChB;AAED,QAAA,MAAM,WAAW,EAAE,aAAa,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAAE,QAAQ,CA4HjE,CAAA;AAED,eAAe,WAAW,CAAA"}
+{"version":3,"file":"next.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/next.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,OAAO,CAAA;AAS1C,UAAU,QAAQ;IAChB,KAAK,CAAC,EAAE,MAAM,CAAA;IACd,MAAM,CAAC,EAAE,MAAM,CAAA;IACf,IAAI,CAAC,EAAE,OAAO,CAAA;IACd,OAAO,CAAC,EAAE,OAAO,CAAA;IACjB,IAAI,CAAC,EAAE,MAAM,CAAA;IACb,KAAK,CAAC,EAAE,OAAO,CAAA;CAChB;AAED,QAAA,MAAM,WAAW,EAAE,aAAa,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAAE,QAAQ,CAsFjE,CAAA;AAED,eAAe,WAAW,CAAA"}

package/dist/cli/commands/next.js

@@ -1,14 +1,9 @@
 import { findProjectRoot } from '../middleware/project-root.js';
 import { resolveOutputMode } from '../middleware/output-mode.js';
 import { createOutputContext } from '../output/context.js';
-import { loadConfig } from '../../config/loader.js';
 import { StateManager } from '../../state/state-manager.js';
-import { discoverMetaPrompts } from '../../core/assembly/meta-prompt-loader.js';
-import { getPackagePipelineDir, getPackageMethodologyDir } from '../../utils/fs.js';
-import { loadAllPresets } from '../../core/assembly/preset-loader.js';
-import { resolveOverlayState } from '../../core/assembly/overlay-state-resolver.js';
-import { buildGraph } from '../../core/dependency/graph.js';
-import { computeEligible } from '../../core/dependency/eligibility.js';
+import { loadPipelineContext } from '../../core/pipeline/context.js';
+import { resolvePipeline } from '../../core/pipeline/resolver.js';
 const nextCommand = {
     command: 'next',
     describe: 'Show next eligible step(s)',
@@ -29,49 +24,22 @@ const nextCommand = {
         }
         const outputMode = resolveOutputMode(argv);
         const output = createOutputContext(outputMode);
-        // 2. Load config and discover meta-prompts
-        const metaPrompts = discoverMetaPrompts(getPackagePipelineDir(projectRoot));
-        const knownSteps = [...metaPrompts.keys()];
-        const { config } = loadConfig(projectRoot, knownSteps);
-        // 3. Load methodology preset and apply project-type overlay
-        const methodologyDir = getPackageMethodologyDir(projectRoot);
-        const presets = loadAllPresets(methodologyDir, knownSteps);
-        const methodology = config?.methodology ?? 'deep';
-        const preset = methodology === 'mvp'
-            ? presets.mvp
-            : methodology === 'custom'
-                ? presets.custom ?? presets.deep
-                : presets.deep;
-        // Apply project-type overlay (e.g., game overlay) if configured
-        const overlayState = config
-            ? resolveOverlayState({
-                config,
-                methodologyDir,
-                metaPrompts,
-                presetSteps: preset?.steps ?? {},
-                output,
-            })
-            : { steps: preset?.steps ?? {} };
-        const presetSteps = new Map(Object.entries(overlayState.steps));
-        // 4. Build graph with preset and compute eligible
-        const computeEligibleFn = (steps) => {
-            const graph = buildGraph([...metaPrompts.values()].map(m => m.frontmatter), presetSteps);
-            return computeEligible(graph, steps);
-        };
-        const stateManager = new StateManager(projectRoot, computeEligibleFn);
+        // 2. Load pipeline context and resolve overlay/graph
+        const context = loadPipelineContext(projectRoot);
+        const pipeline = resolvePipeline(context, { output });
+        const stateManager = new StateManager(projectRoot, pipeline.computeEligible);
         // Reconcile state with current pipeline — adds any new steps that were
         // introduced after the project was initialized.
-        const pipelineSteps = [...metaPrompts.values()].map(m => ({
+        const pipelineSteps = [...context.metaPrompts.values()].map(m => ({
             slug: m.frontmatter.name,
             produces: m.frontmatter.outputs,
             // Steps not in overlay/preset map are disabled. This requires presets to enumerate
             // all known pipeline steps (which they do — see deep.yml/mvp.yml/custom-defaults.yml).
-            enabled: presetSteps.get(m.frontmatter.name)?.enabled ?? false,
+            enabled: pipeline.overlay.steps[m.frontmatter.name]?.enabled ?? false,
         }));
         stateManager.reconcileWithPipeline(pipelineSteps);
         const state = stateManager.loadState();
-        const graph = buildGraph([...metaPrompts.values()].map(m => m.frontmatter), presetSteps);
-        const eligible = computeEligible(graph, state.steps);
+        const eligible = pipeline.computeEligible(state.steps);
         // 4. Apply --count limit
         const count = argv.count ?? eligible.length;
         const shown = eligible.slice(0, count);
@@ -82,7 +50,7 @@ const nextCommand = {
         if (outputMode === 'json') {
             output.result({
                 eligible: shown.map(s => {
-                    const fm = metaPrompts.get(s)?.frontmatter;
+                    const fm = pipeline.stepMeta.get(s);
                     return {
                         slug: s,
                         description: fm?.description ?? '',
@@ -104,7 +72,7 @@ const nextCommand = {
             else {
                 output.info(`Next eligible steps (${shown.length}):`);
                 for (const slug of shown) {
-                    const fm = metaPrompts.get(slug)?.frontmatter;
+                    const fm = pipeline.stepMeta.get(slug);
                     const desc = fm?.summary ?? fm?.description ?? '';
                     output.info(`  scaffold run ${slug}  — ${desc}`);
                 }

package/dist/cli/commands/next.js.map

@@ -1 +1 @@
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package/dist/cli/commands/reset.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"reset.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/reset.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAQ,MAAM,OAAO,CAAA;AAWhD,UAAU,SAAS;IACjB,IAAI,CAAC,EAAE,MAAM,CAAA;IACb,YAAY,CAAC,EAAE,OAAO,CAAA;IACtB,eAAe,CAAC,EAAE,OAAO,CAAA;IACzB,MAAM,CAAC,EAAE,MAAM,CAAA;IACf,IAAI,CAAC,EAAE,OAAO,CAAA;IACd,OAAO,CAAC,EAAE,OAAO,CAAA;IACjB,IAAI,CAAC,EAAE,MAAM,CAAA;IACb,KAAK,CAAC,EAAE,OAAO,CAAA;CAChB;AAED,QAAA,MAAM,YAAY,EAAE,aAAa,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAAE,SAAS,CAiCnE,CAAA;AAgND,eAAe,YAAY,CAAA"}
+{"version":3,"file":"reset.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/reset.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAQ,MAAM,OAAO,CAAA;AAYhD,UAAU,SAAS;IACjB,IAAI,CAAC,EAAE,MAAM,CAAA;IACb,YAAY,CAAC,EAAE,OAAO,CAAA;IACtB,eAAe,CAAC,EAAE,OAAO,CAAA;IACzB,MAAM,CAAC,EAAE,MAAM,CAAA;IACf,IAAI,CAAC,EAAE,OAAO,CAAA;IACd,OAAO,CAAC,EAAE,OAAO,CAAA;IACjB,IAAI,CAAC,EAAE,MAAM,CAAA;IACb,KAAK,CAAC,EAAE,OAAO,CAAA;CAChB;AAED,QAAA,MAAM,YAAY,EAAE,aAAa,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAAE,SAAS,CAiCnE,CAAA;AAkND,eAAe,YAAY,CAAA"}

package/dist/cli/commands/reset.js

@@ -6,7 +6,8 @@ import { createOutputContext } from '../output/context.js';
 import { StateManager } from '../../state/state-manager.js';
 import { acquireLock, releaseLock } from '../../state/lock-manager.js';
 import { findClosestMatch } from '../../utils/levenshtein.js';
-import { buildComputeEligibleFn } from '../../utils/eligible.js';
+import { loadPipelineContext } from '../../core/pipeline/context.js';
+import { resolvePipeline } from '../../core/pipeline/resolver.js';
 const resetCommand = {
     command: 'reset [step]',
     describe: 'Reset a step to pending, or reset entire pipeline state',
@@ -57,7 +58,9 @@ async function resetStep(step, projectRoot, outputMode, output, argv) {
         return;
     }
     try {
-        const stateManager = new StateManager(projectRoot, buildComputeEligibleFn(projectRoot));
+        const context = loadPipelineContext(projectRoot);
+        const pipeline = resolvePipeline(context);
+        const stateManager = new StateManager(projectRoot, pipeline.computeEligible);
         const state = stateManager.loadState();
         // Check step exists in state
         if (!(step in state.steps)) {

package/dist/cli/commands/reset.js.map

@@ -1 +1 @@
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+{"version":3,"file":"reset.js","sourceRoot":"","sources":["../../../src/cli/commands/reset.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,MAAM,SAAS,CAAA;AACxB,OAAO,IAAI,MAAM,WAAW,CAAA;AAC5B,OAAO,EAAE,eAAe,EAAE,MAAM,+BAA+B,CAAA;AAC/D,OAAO,EAAE,iBAAiB,EAAE,MAAM,8BAA8B,CAAA;AAChE,OAAO,EAAE,mBAAmB,EAAE,MAAM,sBAAsB,CAAA;AAC1D,OAAO,EAAE,YAAY,EAAE,MAAM,8BAA8B,CAAA;AAC3D,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,MAAM,6BAA6B,CAAA;AACtE,OAAO,EAAE,gBAAgB,EAAE,MAAM,4BAA4B,CAAA;AAC7D,OAAO,EAAE,mBAAmB,EAAE,MAAM,gCAAgC,CAAA;AACpE,OAAO,EAAE,eAAe,EAAE,MAAM,iCAAiC,CAAA;AAajE,MAAM,YAAY,GAAsD;IACtE,OAAO,EAAE,cAAc;IACvB,QAAQ,EAAE,yDAAyD;IACnE,OAAO,EAAE,CAAC,KAAW,EAAE,EAAE;QACvB,OAAO,KAAK;aACT,UAAU,CAAC,MAAM,EAAE;YAClB,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,8DAA8D;SAC5E,CAAC;aACD,MAAM,CAAC,eAAe,EAAE;YACvB,IAAI,EAAE,SAAS;YACf,WAAW,EAAE,wDAAwD;YACrE,OAAO,EAAE,KAAK;SACf,CAAC,CAAA;IACN,CAAC;IACD,OAAO,EAAE,KAAK,EAAE,IAAI,EAAE,EAAE;QACtB,MAAM,WAAW,GAAG,IAAI,CAAC,IAAI,IAAI,eAAe,CAAC,OAAO,CAAC,GAAG,EAAE,CAAC,CAAA;QAC/D,IAAI,CAAC,WAAW,EAAE,CAAC;YACjB,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,yEAAyE,CAAC,CAAA;YAC/F,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;YACf,OAAM;QACR,CAAC;QAED,MAAM,UAAU,GAAG,iBAAiB,CAAC,IAAI,CAAC,CAAA;QAC1C,MAAM,MAAM,GAAG,mBAAmB,CAAC,UAAU,CAAC,CAAA;QAE9C,kDAAkD;QAClD,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;YACd,MAAM,SAAS,CAAC,IAAI,CAAC,IAAI,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,EAAE,IAAI,CAAC,CAAA;QACnE,CAAC;aAAM,CAAC;YACN,MAAM,aAAa,CAAC,WAAW,EAAE,UAAU,EAAE,MAAM,EAAE,IAAI,CAAC,CAAA;QAC5D,CAAC;IACH,CAAC;CACF,CAAA;AAED;;GAEG;AACH,KAAK,UAAU,SAAS,CACtB,IAAY,EACZ,WAAmB,EACnB,UAAkB,EAClB,MAA6E,EAC7E,IAAe;IAEf,eAAe;IACf,MAAM,UAAU,GAAG,WAAW,CAAC,WAAW,EAAE,OAAO,EAAE,IAAI,CAAC,CAAA;IAC1D,IAAI,CAAC,UAAU,CAAC,QAAQ,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC;QACxC,IAAI,UAAU,CAAC,KAAK,EAAE,CAAC;YACrB,MAAM,CAAC,IAAI,CAAC,GAAG,UAAU,CAAC,KAAK,CAAC,IAAI,KAAK,UAAU,CAAC,KAAK,CAAC,OAAO,EAAE,CAAC,CAAA;QACtE,CAAC;aAAM,CAAC;YACN,MAAM,CAAC,IAAI,CAAC,iCAAiC,CAAC,CAAA;QAChD,CAAC;QACD,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACf,OAAM;IACR,CAAC;IAED,IAAI,CAAC;QACH,MAAM,OAAO,GAAG,mBAAmB,CAAC,WAAW,CAAC,CAAA;QAChD,MAAM,QAAQ,GAAG,eAAe,CAAC,OAAO,CAAC,CAAA;QACzC,MAAM,YAAY,GAAG,IAAI,YAAY,CAAC,WAAW,EAAE,QAAQ,CAAC,eAAe,CAAC,CAAA;QAC5E,MAAM,KAAK,GAAG,YAAY,CAAC,SAAS,EAAE,CAAA;QAEtC,6BAA6B;QAC7B,IAAI,CAAC,CAAC,IAAI,IAAI,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC;YAC3B,MAAM,UAAU,GAAG,gBAAgB,CAAC,IAAI,EAAE,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAA;YACnE,MAAM,GAAG,GAAG,UAAU;gBACpB,CAAC,CAAC,SAAS,IAAI,8BAA8B,UAAU,IAAI;gBAC3D,CAAC,CAAC,SAAS,IAAI,aAAa,CAAA;YAC9B,MAAM,CAAC,KAAK,CAAC;gBACX,IAAI,EAAE,oBAAoB;gBAC1B,OAAO,EAAE,GAAG;gBACZ,QAAQ,EAAE,CAAC;gBACX,QAAQ,EAAE,4CAA4C;aACvD,CAAC,CAAA;YACF,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;YACf,OAAM;QACR,CAAC;QAED,MAAM,SAAS,GAAG,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAEnC,kCAAkC;QAClC,IAAI,SAAS,CAAC,MAAM,KAAK,SAAS,EAAE,CAAC;YACnC,MAAM,CAAC,IAAI,CAAC,SAAS,IAAI,sBAAsB,CAAC,CAAA;YAChD,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;YACf,OAAM;QACR,CAAC;QAED,sBAAsB;QACtB,IAAI,SAAS,CAAC,MAAM,KAAK,aAAa,EAAE,CAAC;YACvC,MAAM,CAAC,IAAI,CACT,SAAS,IAAI,6EAA6E,CAC3F,CAAA;QACH,CAAC;QAED,0CAA0C;QAC1C,IAAI,SAAS,CAAC,MAAM,KAAK,WAAW,IAAI,UAAU,KAAK,aAAa,EAAE,CAAC;YACrE,MAAM,OAAO,GAAG,MAAM,MAAM,CAAC,OAAO,CAClC,SAAS,IAAI,kEAAkE,EAC/E,KAAK,CACN,CAAA;YACD,IAAI,CAAC,OAAO,EAAE,CAAC;gBACb,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;gBACf,OAAM;YACR,CAAC;QACH,CAAC;aAAM,IAAI,SAAS,CAAC,MAAM,KAAK,WAAW,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC;YAC3D,MAAM,CAAC,KAAK,CAAC;gBACX,IAAI,EAAE,wBAAwB;gBAC9B,OAAO,EAAE,SAAS,IAAI,uCAAuC;gBAC7D,QAAQ,EAAE,CAAC;gBACX,QAAQ,EAAE,uCAAuC;aAClD,CAAC,CAAA;YACF,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;YACf,OAAM;QACR,CAAC;QAED,wBAAwB;QACxB,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG;YAClB,MAAM,EAAE,SAAS;YACjB,MAAM,EAAE,SAAS,CAAC,MAAM,IAAI,UAAU;YACtC,QAAQ,EAAE,SAAS,CAAC,QAAQ,IAAI,EAAE;SACnC,CAAA;QAED,+CAA+C;QAC/C,IAAI,KAAK,CAAC,WAAW,EAAE,IAAI,KAAK,IAAI,EAAE,CAAC;YACrC,KAAK,CAAC,WAAW,GAAG,IAAI,CAAA;QAC1B,CAAC;QAED,YAAY,CAAC,SAAS,CAAC,KAAK,CAAC,CAAA;QAE7B,IAAI,UAAU,KAAK,MAAM,EAAE,CAAC;YAC1B,MAAM,CAAC,MAAM,CAAC;gBACZ,IAAI;gBACJ,cAAc,EAAE,SAAS,CAAC,MAAM;gBAChC,SAAS,EAAE,SAAS;aACrB,CAAC,CAAA;QACJ,CAAC;aAAM,CAAC;YACN,MAAM,CAAC,OAAO,CAAC,SAAS,IAAI,oBAAoB,CAAC,CAAA;YACjD,MAAM,CAAC,IAAI,CAAC,2CAA2C,CAAC,CAAA;QAC1D,CAAC;QACD,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IACjB,CAAC;YAAS,CAAC;QACT,IAAI,UAAU,CAAC,QAAQ,EAAE,CAAC;YACxB,WAAW,CAAC,WAAW,CAAC,CAAA;QAC1B,CAAC;IACH,CAAC;AACH,CAAC;AAED;;GAEG;AACH,KAAK,UAAU,aAAa,CAC1B,WAAmB,EACnB,UAAkB,EAClB,MAA6E,EAC7E,IAAe;IAEf,MAAM,WAAW,GAAG,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE,WAAW,CAAC,CAAA;IAEvD,qBAAqB;IACrB,MAAM,cAAc,GAAG,IAAI,CAAC,eAAe,CAAC,KAAK,IAAI,IAAI,IAAI,CAAC,YAAY,KAAK,IAAI,CAAA;IAEnF,IAAI,UAAU,KAAK,aAAa,EAAE,CAAC;QACjC,MAAM,SAAS,GAAG,MAAM,MAAM,CAAC,OAAO,CACpC,gEAAgE,EAChE,KAAK,CACN,CAAA;QACD,IAAI,CAAC,SAAS,EAAE,CAAC;YACf,MAAM,CAAC,IAAI,CAAC,kBAAkB,CAAC,CAAA;YAC/B,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;YACf,OAAM;QACR,CAAC;IACH,CAAC;SAAM,IAAI,CAAC,cAAc,EAAE,CAAC;QAC3B,MAAM,CAAC,KAAK,CAAC;YACX,IAAI,EAAE,wBAAwB;YAC9B,OAAO,EAAE,wDAAwD;YACjE,QAAQ,EAAE,CAAC;YACX,QAAQ,EAAE,0BAA0B;SACrC,CAAC,CAAA;QACF,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACf,OAAM;I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package/dist/cli/commands/rework.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"rework.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/rework.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAQ,MAAM,OAAO,CAAA;AAmBhD,UAAU,UAAU;IAClB,MAAM,CAAC,EAAE,MAAM,CAAA;IACf,OAAO,CAAC,EAAE,MAAM,CAAA;IAChB,OAAO,CAAC,EAAE,MAAM,CAAA;IAChB,KAAK,CAAC,EAAE,MAAM,CAAA;IACd,GAAG,CAAC,EAAE,OAAO,CAAA;IACb,KAAK,CAAC,EAAE,OAAO,CAAA;IACf,IAAI,CAAC,EAAE,OAAO,CAAA;IACd,MAAM,CAAC,EAAE,OAAO,CAAA;IAChB,KAAK,CAAC,EAAE,OAAO,CAAA;IACf,OAAO,CAAC,EAAE,MAAM,CAAA;IAChB,MAAM,CAAC,EAAE,MAAM,CAAA;IACf,OAAO,CAAC,EAAE,OAAO,CAAA;IACjB,IAAI,CAAC,EAAE,MAAM,CAAA;IACb,KAAK,CAAC,EAAE,OAAO,CAAA;CAChB;AAED,QAAA,MAAM,aAAa,EAAE,aAAa,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAAE,UAAU,CA6VrE,CAAA;AAED,eAAe,aAAa,CAAA"}
+{"version":3,"file":"rework.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/rework.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAQ,MAAM,OAAO,CAAA;AAehD,UAAU,UAAU;IAClB,MAAM,CAAC,EAAE,MAAM,CAAA;IACf,OAAO,CAAC,EAAE,MAAM,CAAA;IAChB,OAAO,CAAC,EAAE,MAAM,CAAA;IAChB,KAAK,CAAC,EAAE,MAAM,CAAA;IACd,GAAG,CAAC,EAAE,OAAO,CAAA;IACb,KAAK,CAAC,EAAE,OAAO,CAAA;IACf,IAAI,CAAC,EAAE,OAAO,CAAA;IACd,MAAM,CAAC,EAAE,OAAO,CAAA;IAChB,KAAK,CAAC,EAAE,OAAO,CAAA;IACf,OAAO,CAAC,EAAE,MAAM,CAAA;IAChB,MAAM,CAAC,EAAE,MAAM,CAAA;IACf,OAAO,CAAC,EAAE,OAAO,CAAA;IACjB,IAAI,CAAC,EAAE,MAAM,CAAA;IACb,KAAK,CAAC,EAAE,OAAO,CAAA;CAChB;AAED,QAAA,MAAM,aAAa,EAAE,aAAa,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAAE,UAAU,CA2TrE,CAAA;AAED,eAAe,aAAa,CAAA"}

package/dist/cli/commands/rework.js

@@ -1,16 +1,12 @@
 import { findProjectRoot } from '../middleware/project-root.js';
 import { resolveOutputMode } from '../middleware/output-mode.js';
 import { createOutputContext } from '../output/context.js';
+import { displayErrors } from '../output/error-display.js';
 import { acquireLock, releaseLock } from '../../state/lock-manager.js';
 import { ReworkManager } from '../../state/rework-manager.js';
 import { StateManager } from '../../state/state-manager.js';
-import { discoverMetaPrompts } from '../../core/assembly/meta-prompt-loader.js';
-import { getPackagePipelineDir, getPackageMethodologyDir } from '../../utils/fs.js';
-import { loadConfig } from '../../config/loader.js';
-import { loadAllPresets } from '../../core/assembly/preset-loader.js';
-import { resolveOverlayState } from '../../core/assembly/overlay-state-resolver.js';
-import { buildGraph } from '../../core/dependency/graph.js';
-import { computeEligible } from '../../core/dependency/eligibility.js';
+import { loadPipelineContext } from '../../core/pipeline/context.js';
+import { resolvePipeline } from '../../core/pipeline/resolver.js';
 import { parsePhases, parseThrough, applyExclusions, resolveStepsForPhases } from '../../core/rework/phase-selector.js';
 import { PHASES } from '../../types/frontmatter.js';
 const reworkCommand = {
@@ -239,48 +235,19 @@ const reworkCommand = {
             return;
         }
         try {
-            // Load config and pipeline
-            const { config, errors: configErrors } = loadConfig(projectRoot, []);
-            if (!config) {
-                for (const err of configErrors) {
-                    output.error(err);
-                }
+            // Load pipeline context and resolve overlay/graph
+            const context = loadPipelineContext(projectRoot);
+            if (!context.config) {
+                displayErrors(context.configErrors, context.configWarnings, output);
                 process.exit(1);
                 return;
             }
-            const pipelineDir = getPackagePipelineDir(projectRoot);
-            const metaPrompts = discoverMetaPrompts(pipelineDir);
-            const metaPromptList = [...metaPrompts.values()].map(m => m.frontmatter);
-            const methodologyDir = getPackageMethodologyDir(projectRoot);
-            const presets = loadAllPresets(methodologyDir, [...metaPrompts.keys()]);
-            const preset = config.methodology === 'mvp'
-                ? presets.mvp
-                : config.methodology === 'custom'
-                    ? presets.custom ?? presets.deep
-                    : presets.deep;
-            const resolvedPreset = preset ?? {
-                name: 'deep',
-                description: 'Default deep methodology',
-                default_depth: 3,
-                steps: {},
-            };
-            // Apply project-type overlay (e.g., game overlay) if configured
-            const overlayState = resolveOverlayState({
-                config,
-                methodologyDir,
-                metaPrompts,
-                presetSteps: resolvedPreset.steps,
-                output,
-            });
-            // Build graph with overlay-aware steps
-            const presetStepsMap = new Map(Object.entries(overlayState.steps));
-            const graph = buildGraph(metaPromptList, presetStepsMap);
-            // Load state
-            const computeEligibleFn = (steps) => computeEligible(graph, steps);
-            const stateManager = new StateManager(projectRoot, computeEligibleFn);
+            const pipeline = resolvePipeline(context, { output });
+            const stateManager = new StateManager(projectRoot, pipeline.computeEligible);
             const state = stateManager.loadState();
+            const metaPromptList = [...context.metaPrompts.values()].map(m => m.frontmatter);
             // Resolve steps for selected phases
-            const reworkSteps = resolveStepsForPhases(phaseNumbers, metaPromptList, state, graph);
+            const reworkSteps = resolveStepsForPhases(phaseNumbers, metaPromptList, state, pipeline.graph);
             if (reworkSteps.length === 0) {
                 output.error({
                     code: 'REWORK_NO_STEPS',

package/dist/cli/commands/rework.js.map

@@ -1 +1 @@
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package/dist/cli/commands/run.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"run.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/run.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAQ,aAAa,EAAE,MAAM,OAAO,CAAA;AA+BhD,UAAU,OAAO;IACf,IAAI,EAAE,MAAM,CAAA;IACZ,KAAK,CAAC,EAAE,MAAM,CAAA;IACd,YAAY,CAAC,EAAE,MAAM,CAAA;IACrB,KAAK,CAAC,EAAE,OAAO,CAAA;IACf,MAAM,CAAC,EAAE,MAAM,CAAA;IACf,IAAI,CAAC,EAAE,OAAO,CAAA;IACd,OAAO,CAAC,EAAE,OAAO,CAAA;IACjB,IAAI,CAAC,EAAE,MAAM,CAAA;CACd;AAED,QAAA,MAAM,UAAU,EAAE,aAAa,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAAE,OAAO,CAif/D,CAAA;AAED,eAAe,UAAU,CAAA"}
+{"version":3,"file":"run.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/run.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAQ,aAAa,EAAE,MAAM,OAAO,CAAA;AAwBhD,UAAU,OAAO;IACf,IAAI,EAAE,MAAM,CAAA;IACZ,KAAK,CAAC,EAAE,MAAM,CAAA;IACd,YAAY,CAAC,EAAE,MAAM,CAAA;IACrB,KAAK,CAAC,EAAE,OAAO,CAAA;IACf,MAAM,CAAC,EAAE,MAAM,CAAA;IACf,IAAI,CAAC,EAAE,OAAO,CAAA;IACd,OAAO,CAAC,EAAE,OAAO,CAAA;IACjB,IAAI,CAAC,EAAE,MAAM,CAAA;CACd;AAED,QAAA,MAAM,UAAU,EAAE,aAAa,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAAE,OAAO,CAsc/D,CAAA;AAED,eAAe,UAAU,CAAA"}

package/dist/cli/commands/run.js

@@ -4,19 +4,15 @@ import { StateManager } from '../../state/state-manager.js';
 import { acquireLock, releaseLock } from '../../state/lock-manager.js';
 import { analyzeCrash } from '../../state/completion.js';
 import { AssemblyEngine } from '../../core/assembly/engine.js';
-import { discoverAllMetaPrompts } from '../../core/assembly/meta-prompt-loader.js';
-import { getPackagePipelineDir, getPackageMethodologyDir, getPackageKnowledgeDir, getPackageToolsDir, } from '../../utils/fs.js';
+import { getPackageKnowledgeDir } from '../../utils/fs.js';
 import { buildIndexWithOverrides, loadEntries } from '../../core/assembly/knowledge-loader.js';
 import { loadInstructions } from '../../core/assembly/instruction-loader.js';
 import { resolveDepth } from '../../core/assembly/depth-resolver.js';
 import { detectUpdateMode } from '../../core/assembly/update-mode.js';
 import { detectMethodologyChange } from '../../core/assembly/methodology-change.js';
-import { loadAllPresets } from '../../core/assembly/preset-loader.js';
-import { resolveOverlayState } from '../../core/assembly/overlay-state-resolver.js';
-import { loadConfig } from '../../config/loader.js';
-import { buildGraph } from '../../core/dependency/graph.js';
-import { detectCycles, topologicalSort } from '../../core/dependency/dependency.js';
-import { computeEligible } from '../../core/dependency/eligibility.js';
+import { detectCycles } from '../../core/dependency/dependency.js';
+import { loadPipelineContext } from '../../core/pipeline/context.js';
+import { resolvePipeline } from '../../core/pipeline/resolver.js';
 import { findProjectRoot } from '../../cli/middleware/project-root.js';
 import { createOutputContext } from '../../cli/output/context.js';
 import { displayErrors } from '../../cli/output/error-display.js';
@@ -60,15 +56,18 @@ const runCommand = {
         const outputMode = resolveOutputMode(argv);
         const output = createOutputContext(outputMode);
         // -----------------------------------------------------------------------
-        // Step 2: Discover meta-prompts and pipeline (before config so we have
-        //         real step names for Phase-6 custom.steps validation)
+        // Step 2: Load pipeline context and resolve overlay/graph
         // -----------------------------------------------------------------------
-        const pipelineDir = getPackagePipelineDir(projectRoot);
-        const toolsDir = getPackageToolsDir(projectRoot);
-        const metaPrompts = discoverAllMetaPrompts(pipelineDir, toolsDir);
-        const metaPrompt = metaPrompts.get(step);
+        const context = loadPipelineContext(projectRoot, { includeTools: true });
+        if (!context.config) {
+            displayErrors(context.configErrors, context.configWarnings, output);
+            process.exit(1);
+            return;
+        }
+        const pipeline = resolvePipeline(context, { output });
+        const metaPrompt = context.metaPrompts.get(step);
         if (!metaPrompt) {
-            const candidates = [...metaPrompts.keys()];
+            const candidates = [...context.metaPrompts.keys()];
             const suggestion = findClosestMatch(step, candidates, 3);
             const suggestionText = suggestion ? ` Did you mean '${suggestion}'?` : '';
             output.error({
@@ -79,35 +78,6 @@ const runCommand = {
             });
             process.exit(1);
         }
-        const knownSteps = [...metaPrompts.keys()];
-        const { config, errors: configErrors } = loadConfig(projectRoot, knownSteps);
-        if (!config) {
-            displayErrors(configErrors, [], output);
-            process.exit(1);
-        }
-        const methodologyDir = getPackageMethodologyDir(projectRoot);
-        const presets = loadAllPresets(methodologyDir, [...metaPrompts.keys()]);
-        const preset = config.methodology === 'mvp'
-            ? presets.mvp
-            : config.methodology === 'custom'
-                ? presets.custom ?? presets.deep
-                : presets.deep;
-        const resolvedPreset = preset ?? {
-            name: 'deep',
-            description: 'Default deep methodology',
-            default_depth: 3,
-            steps: {},
-        };
-        // -----------------------------------------------------------------------
-        // Step 2b: Load and apply project-type overlay (if configured)
-        // -----------------------------------------------------------------------
-        const overlayState = resolveOverlayState({
-            config,
-            methodologyDir,
-            metaPrompts,
-            presetSteps: resolvedPreset.steps,
-            output,
-        });
         // -----------------------------------------------------------------------
         // Step 3: Acquire lock
         // -----------------------------------------------------------------------
@@ -133,11 +103,7 @@ const runCommand = {
         // -----------------------------------------------------------------------
         // Step 4: Load and validate state
         // -----------------------------------------------------------------------
-        const computeEligibleFn = (steps) => {
-            const graph = buildGraph([...metaPrompts.values()].map(m => m.frontmatter), new Map(Object.entries(overlayState.steps)));
-            return computeEligible(graph, steps);
-        };
-        const stateManager = new StateManager(projectRoot, computeEligibleFn);
+        const stateManager = new StateManager(projectRoot, pipeline.computeEligible);
         let state = stateManager.loadState();
         // Crash recovery: in_progress is non-null from a previous run
         if (state.in_progress !== null) {
@@ -183,8 +149,7 @@ const runCommand = {
         // -----------------------------------------------------------------------
         // Step 5: Check dependencies
         // -----------------------------------------------------------------------
-        const presetStepsMap = new Map(Object.entries(overlayState.steps));
-        const graph = buildGraph([...metaPrompts.values()].map(m => m.frontmatter), presetStepsMap);
+        const { graph } = pipeline;
         const cycles = detectCycles(graph);
         if (cycles.length > 0) {
             displayErrors(cycles, [], output);
@@ -192,11 +157,12 @@ const runCommand = {
                 releaseLock(projectRoot);
             process.exit(1);
         }
-        topologicalSort(graph);
         // Tools (category: 'tool') are not in the dependency graph — skip dep checking
         const isTool = metaPrompt.frontmatter.category === 'tool';
         const stepNode = isTool ? undefined : graph.nodes.get(step);
-        const deps = overlayState.dependencies[step] ?? stepNode?.dependencies ?? metaPrompt.frontmatter.dependencies ?? [];
+        const deps = isTool
+            ? (pipeline.overlay.dependencies[step] ?? [])
+            : (stepNode?.dependencies ?? []);
         if (!isTool) {
             const unmetDeps = deps.filter(dep => {
                 // Overlay-disabled deps are treated as satisfied (matches eligibility.ts)
@@ -222,7 +188,7 @@ const runCommand = {
         // Step 6: Check update mode and depth downgrade
         // -----------------------------------------------------------------------
         const cliDepth = argv.depth !== undefined ? argv.depth : undefined;
-        const { depth, provenance } = resolveDepth(step, config, resolvedPreset, cliDepth);
+        const { depth, provenance } = resolveDepth(step, context.config, pipeline.preset, cliDepth);
         const updateModeResult = detectUpdateMode({ step, state, currentDepth: depth, projectRoot });
         if (updateModeResult.isUpdateMode) {
             if (!argv.force) {
@@ -257,7 +223,7 @@ const runCommand = {
             }
         }
         // Check methodology change
-        const methodologyChangeResult = detectMethodologyChange({ state, config });
+        const methodologyChangeResult = detectMethodologyChange({ state, config: context.config });
         for (const w of methodologyChangeResult.warnings) {
             output.warn(w);
         }
@@ -276,7 +242,7 @@ const runCommand = {
             // -----------------------------------------------------------------------
             const { instructions } = loadInstructions(projectRoot, step, argv.instructions);
             const kbIndex = buildIndexWithOverrides(projectRoot, getPackageKnowledgeDir(projectRoot));
-            const { entries: knowledgeEntries, warnings: kbWarnings } = loadEntries(kbIndex, overlayState.knowledge[step] ?? metaPrompt.frontmatter.knowledgeBase ?? []);
+            const { entries: knowledgeEntries, warnings: kbWarnings } = loadEntries(kbIndex, pipeline.overlay.knowledge[step] ?? metaPrompt.frontmatter.knowledgeBase ?? []);
             for (const w of kbWarnings) {
                 output.warn(w);
             }
@@ -307,7 +273,7 @@ const runCommand = {
             // Gather artifacts from reads (optional cross-cutting references)
             // Note: graph defaults missing steps to enabled:true, which may not reflect
             // custom config overrides. This is a pre-existing graph builder limitation.
-            const reads = overlayState.reads[step] ?? metaPrompt.frontmatter.reads ?? [];
+            const reads = pipeline.overlay.reads[step] ?? metaPrompt.frontmatter.reads ?? [];
             for (const readStep of reads) {
                 // Check dependency graph for enablement (overlay-disabled steps)
                 const readNode = graph?.nodes.get(readStep);
@@ -356,7 +322,7 @@ const runCommand = {
             // -----------------------------------------------------------------------
             const engine = new AssemblyEngine();
             const assemblyResult = engine.assemble(step, {
-                config,
+                config: context.config,
                 state,
                 metaPrompt,
                 knowledgeEntries,
@@ -394,7 +360,7 @@ const runCommand = {
                     else {
                         // Reload state for next eligible
                         const stateForEligible = stateManager.loadState();
-                        const nextSteps = computeEligible(graph, stateForEligible.steps);
+                        const nextSteps = pipeline.computeEligible(stateForEligible.steps);
                         output.result({
                             step,
                             status: 'in_progress',
@@ -449,7 +415,7 @@ const runCommand = {
             // Step 12: Show next eligible steps
             // -----------------------------------------------------------------------
             const finalState = stateManager.loadState();
-            const nextSteps = computeEligible(graph, finalState.steps);
+            const nextSteps = pipeline.computeEligible(finalState.steps);
             if (outputMode === 'interactive') {
                 if (nextSteps.length > 0) {
                     output.info(`Next eligible: ${nextSteps.join(', ')}`);