intentdna 1.2.1 → 1.2.3

package/dist/audit/index.d.ts

@@ -106,4 +106,3 @@ export declare function generateAuditSummary(logDir: string, from: string, to: s
  * Render audit summary as markdown.
  */
 export declare function renderAuditReport(summary: AuditSummary): string;
-//# sourceMappingURL=index.d.ts.map

package/dist/audit/index.js

@@ -141,4 +141,3 @@ export function renderAuditReport(summary) {
     }
     return lines.join("\n");
 }
-//# sourceMappingURL=index.js.map

package/dist/cli/commands/compile.d.ts

@@ -11,4 +11,3 @@ export interface CompileOptions {
     ir: boolean;
 }
 export declare function runCompile(opts: CompileOptions): Promise<number>;
-//# sourceMappingURL=compile.d.ts.map

package/dist/cli/commands/compile.js

@@ -86,4 +86,3 @@ export async function runCompile(opts) {
         return 1;
     }
 }
-//# sourceMappingURL=compile.js.map

package/dist/cli/commands/epigenetic.d.ts

@@ -17,4 +17,3 @@ export interface EpigeneticOptions {
     json?: boolean;
 }
 export declare function runEpigenetic(opts: EpigeneticOptions): Promise<number>;
-//# sourceMappingURL=epigenetic.d.ts.map

package/dist/cli/commands/epigenetic.js

@@ -109,4 +109,3 @@ async function doMarkers(engine, opts) {
     }
     return 0;
 }
-//# sourceMappingURL=epigenetic.js.map

package/dist/cli/commands/evolve.d.ts

@@ -9,4 +9,3 @@ export interface EvolveOptions {
     storeDir?: string;
 }
 export declare function runEvolve(opts: EvolveOptions): Promise<number>;
-//# sourceMappingURL=evolve.d.ts.map

package/dist/cli/commands/evolve.js

@@ -49,4 +49,3 @@ export async function runEvolve(opts) {
         return 1;
     }
 }
-//# sourceMappingURL=evolve.js.map

package/dist/cli/commands/guard.d.ts

@@ -19,4 +19,3 @@ export interface GuardOptions {
     remove: boolean;
 }
 export declare function runGuard(opts: GuardOptions): Promise<number>;
-//# sourceMappingURL=guard.d.ts.map

package/dist/cli/commands/guard.js

@@ -177,7 +177,6 @@ export async function runGuard(opts) {
             const r = await runSync({
                 files: [], target: "claude-md",
                 inject: join(cwd, "CLAUDE.md"),
-                hooksDir: join(cwd, ".claude", "hooks"),
                 evolve: false, remove: true,
             });
             if (r !== 0)
@@ -215,7 +214,6 @@ export async function runGuard(opts) {
                 files: [tmpFile],
                 target: "claude-md",
                 inject: join(cwd, "CLAUDE.md"),
-                hooksDir: join(cwd, ".claude", "hooks"),
                 evolve: false, remove: false,
             });
             if (r !== 0)
@@ -254,4 +252,3 @@ export async function runGuard(opts) {
         await rm(tmpFile, { force: true });
     }
 }
-//# sourceMappingURL=guard.js.map

package/dist/cli/commands/import.d.ts

@@ -68,4 +68,3 @@ export declare function parseClaudeMD(content: string): {
 export declare function importHarness(dir: string): Promise<ImportResult>;
 export declare function generateDNAYaml(result: ImportResult, projectName?: string): string;
 export declare function runImport(opts: ImportOptions): Promise<number>;
-//# sourceMappingURL=import.d.ts.map

package/dist/cli/commands/import.js

@@ -426,4 +426,3 @@ async function safeReaddir(path) {
         return [];
     }
 }
-//# sourceMappingURL=import.js.map

package/dist/cli/commands/init.d.ts

@@ -12,4 +12,3 @@ export interface InitOptions {
     upgrade?: string | boolean;
 }
 export declare function runInit(opts: InitOptions): Promise<number>;
-//# sourceMappingURL=init.d.ts.map

package/dist/cli/commands/init.js

@@ -364,4 +364,3 @@ export async function runInit(opts) {
         return 1;
     }
 }
-//# sourceMappingURL=init.js.map

package/dist/cli/commands/run.d.ts

@@ -56,4 +56,3 @@ export declare function executeGroup(group: ParallelGroup, allSteps: WorkflowSte
 export declare function checkRetryNeeded(stepResults: Map<string, StepResult>, transitions: TransitionRule[]): boolean;
 export declare function runRun(opts: RunOptions): Promise<number>;
 export {};
-//# sourceMappingURL=run.d.ts.map

package/dist/cli/commands/run.js

@@ -13,7 +13,7 @@ import { loadDNA, compileFromFiles } from "../../compiler/index.js";
 import { cascadeDNA } from "../../compiler/cascade.js";
 import { compileWorkflow } from "../../compiler/workflow.js";
 import { compileAllRolesToAgentMD, writeAgentMDFiles, toKebabCase, } from "../../runtime/agent-md.js";
-import { compileToHooks, writeHookScripts } from "../../runtime/hooks.js";
+import { createCompiledIR, writeCompiledIR } from "../../runtime/plugin-adapter.js";
 // ── Template & Condition Helpers ───────────────────────────
 /**
  * Replace {{var}} placeholders in a template string.
@@ -127,21 +127,6 @@ export async function executeStep(step, vars, opts) {
         "--no-session-persistence",
     ];
     log(`Running step: ${step.id} (agent: ${agentName})`);
-    // Write mode file if step declares a mode
-    if (step.mode) {
-        const modeData = JSON.stringify({
-            active_mode: step.mode,
-            set_at: new Date().toISOString(),
-            set_by: `run:${step.id}`,
-        });
-        try {
-            const { mkdir: mkdirAsync, writeFile: writeFileAsync } = await import("node:fs/promises");
-            await mkdirAsync(".dna", { recursive: true });
-            await writeFileAsync(".dna/mode", modeData, "utf-8");
-            log(`Mode set: ${step.mode}`);
-        }
-        catch { /* best effort */ }
-    }
     try {
         const output = await spawnAsync("claude", args, prompt);
         await writeFile(resultFile, output, "utf-8");
@@ -271,7 +256,6 @@ export async function runRun(opts) {
     const maxBudget = opts.maxBudget ?? 5;
     const permissionMode = opts.permissionMode ?? "bypassPermissions";
     const agentsDir = opts.agentsDir ?? ".claude/agents";
-    const hooksDir = opts.hooksDir ?? ".claude/hooks";
     try {
         // ── Step 1: Load & compile DNA ───────────────────────
         log("Loading DNA files...");
@@ -311,9 +295,9 @@ export async function runRun(opts) {
         const agentResults = compileAllRolesToAgentMD(cascaded.roles, ir);
         await writeAgentMDFiles(agentResults, agentsDir);
         log(`Generated ${agentResults.length} agent file(s) in ${agentsDir}`);
-        const hookScripts = compileToHooks(ir);
-        await writeHookScripts(hooksDir, hookScripts);
-        log(`Generated hook scripts in ${hooksDir}`);
+        const hookScripts = createCompiledIR(ir, cascaded.roles);
+        await writeCompiledIR(process.cwd(), hookScripts);
+        log("Synced compiled IR for dna-hook enforcement");
         // ── Step 5: Prepare log directory ────────────────────
         const timestamp = new Date().toISOString().replace(/[:.]/g, "-");
         const logDir = opts.logDir ?? join(".intentdna", "runs", `${opts.workflowName}-${timestamp}`);
@@ -367,12 +351,6 @@ export async function runRun(opts) {
             // All passed
             break;
         }
-        // Clean up mode file after workflow completes
-        try {
-            const { rm: rmAsync } = await import("node:fs/promises");
-            await rmAsync(".dna/mode", { force: true });
-        }
-        catch { /* best effort */ }
         return printSummary(stepResults, round, logDir, 0);
     }
     catch (err) {
@@ -428,4 +406,3 @@ function printSummary(results, rounds, logDir, exitCode) {
     process.stderr.write(`\nTotal: ${passed} passed, ${failed} failed, ${skipped} skipped\n`);
     return exitCode;
 }
-//# sourceMappingURL=run.js.map

package/dist/cli/commands/show.d.ts

@@ -9,4 +9,3 @@ export interface ShowOptions {
     json: boolean;
 }
 export declare function runShow(opts: ShowOptions): Promise<number>;
-//# sourceMappingURL=show.d.ts.map

package/dist/cli/commands/show.js

@@ -75,4 +75,3 @@ export async function runShow(opts) {
         return 1;
     }
 }
-//# sourceMappingURL=show.js.map

package/dist/cli/commands/sync.d.ts

@@ -26,6 +26,6 @@ export interface SyncOptions {
     settingsPath?: string;
     lockFile?: string;
     remove: boolean;
+    plugin?: boolean;
 }
 export declare function runSync(opts: SyncOptions): Promise<number>;
-//# sourceMappingURL=sync.d.ts.map

package/dist/cli/commands/sync.js

@@ -11,17 +11,17 @@
  * Targets: claude-md, soul-md, cursorrules, system-prompt
  */
 import { resolve, dirname } from "node:path";
-import { readFile, writeFile as writeFileAsync, stat, mkdir } from "node:fs/promises";
+import { readFile, writeFile as writeFileAsync, stat, mkdir, readdir, unlink, rm } from "node:fs/promises";
 import { createHash } from "node:crypto";
 import { fileURLToPath } from "node:url";
 import { createInterface } from "node:readline";
 import { loadDNA, compileFromFiles } from "../../compiler/index.js";
 import { compileToMarkdown, injectIntoFile, removeFromFile } from "../../runtime/markdown.js";
-import { compileToHooks, writeHookScripts, removeHookScripts } from "../../runtime/hooks.js";
 import { compileAllRolesToAgentMD, writeAgentMDFiles, removeAgentMDFiles } from "../../runtime/agent-md.js";
 import { removeWorkflowScripts } from "../../runtime/workflow-runner.js";
 import { compileWorkflowToSkill, writeSkillFiles } from "../../runtime/skill-adapter.js";
-import { compileSettingsFromHooks, mergeSettingsFile } from "../../runtime/settings-adapter.js";
+import { compilePluginSettings, detectEnabledEvents, mergeSettingsFile } from "../../runtime/settings-adapter.js";
+import { createCompiledIR, writeCompiledIR } from "../../runtime/plugin-adapter.js";
 import { cascadeDNA } from "../../compiler/cascade.js";
 import { EvolutionEngine } from "../../evolution/index.js";
 const VALID_TARGETS = ["claude-md", "soul-md", "cursorrules", "system-prompt"];
@@ -34,6 +34,65 @@ async function fileExists(path) {
         return false;
     }
 }
+const DNA_SENTINEL = "intentdna:managed";
+const LEGACY_BASH_HOOKS = [
+    "dna-pre-tool-use.sh",
+    "dna-post-tool-use.sh",
+    "dna-user-prompt-submit.sh",
+    "dna-subagent-stop.sh",
+    "dna-pre-compact.sh",
+    "dna-notification.sh",
+];
+/**
+ * Remove legacy bash hook scripts written by previous Intent DNA versions.
+ * Only removes files that contain the sentinel comment.
+ */
+async function removeLegacyBashHooks(hooksDir) {
+    let removed = 0;
+    for (const file of LEGACY_BASH_HOOKS) {
+        const path = resolve(hooksDir, file);
+        try {
+            const content = await readFile(path, "utf-8");
+            if (content.includes("intentdna:managed")) {
+                await unlink(path);
+                removed++;
+            }
+        }
+        catch { /* File doesn't exist, skip */ }
+    }
+    return removed;
+}
+/**
+ * Remove stale DNA-managed files from a directory.
+ * Scans for files/dirs containing the sentinel marker and deletes them.
+ * Returns list of removed paths.
+ */
+async function cleanStaleDNAFiles(dir, type) {
+    const removed = [];
+    try {
+        const entries = await readdir(dir, { withFileTypes: true });
+        for (const entry of entries) {
+            const fullPath = resolve(dir, entry.name);
+            if (type === "agents" && entry.isFile() && entry.name.endsWith(".md")) {
+                const content = await readFile(fullPath, "utf-8").catch(() => "");
+                if (content.includes(DNA_SENTINEL)) {
+                    await unlink(fullPath);
+                    removed.push(fullPath);
+                }
+            }
+            else if (type === "skills" && entry.isDirectory()) {
+                const skillFile = resolve(fullPath, "SKILL.md");
+                const content = await readFile(skillFile, "utf-8").catch(() => "");
+                if (content.includes(DNA_SENTINEL)) {
+                    await rm(fullPath, { recursive: true, force: true });
+                    removed.push(fullPath);
+                }
+            }
+        }
+    }
+    catch { /* dir doesn't exist yet */ }
+    return removed;
+}
 /**
  * Prompt user for a single variable value.
  */
@@ -180,11 +239,10 @@ export async function runSync(opts) {
         const hasClaudeMd = await fileExists(resolve(cwd, "CLAUDE.md"));
         if (hasClaudeDir || hasClaudeMd || opts.files.length > 0) {
             opts.inject = resolve(cwd, "CLAUDE.md");
-            opts.hooksDir = resolve(cwd, ".claude", "hooks");
             opts.agentsDir = resolve(cwd, ".claude", "agents");
             opts.skillsDir = resolve(cwd, ".claude", "skills");
             opts.settingsPath = resolve(cwd, ".claude", "settings.json");
-            process.stderr.write(`Auto-detect: Claude Code → CLAUDE.md + hooks + agents + skills + settings\n`);
+            process.stderr.write(`Auto-detect: Claude Code → CLAUDE.md + agents + skills + settings\n`);
         }
     }
     // Handle --remove
@@ -203,12 +261,12 @@ export async function runSync(opts) {
             }
         }
         if (opts.hooksDir) {
-            const count = await removeHookScripts(opts.hooksDir);
+            const count = await removeLegacyBashHooks(opts.hooksDir);
             if (count > 0) {
-                process.stderr.write(`Removed ${count} Intent DNA hook script(s) from ${opts.hooksDir}\n`);
+                process.stderr.write(`Removed ${count} legacy bash hook(s) from ${opts.hooksDir}\n`);
             }
             else {
-                process.stderr.write(`No Intent DNA hook scripts found in ${opts.hooksDir}\n`);
+                process.stderr.write(`No legacy bash hooks found in ${opts.hooksDir}\n`);
             }
         }
         if (opts.agentsDir) {
@@ -282,28 +340,41 @@ export async function runSync(opts) {
             }
             trackedOutputs.push(resolve(opts.inject));
         }
-        // Step 4: Generate hook scripts
-        if (opts.hooksDir) {
-            const scripts = compileToHooks(ir);
-            const written = await writeHookScripts(opts.hooksDir, scripts);
-            if (written.length > 0) {
-                process.stderr.write(`Generated ${written.length} hook script(s) in ${opts.hooksDir}\n`);
-                for (const f of written) {
-                    process.stderr.write(`  ${f}\n`);
-                }
-                trackedOutputs.push(...written.map(f => resolve(f)));
-                // Report role scope information
-                if (ir.roles_scope_map && ir.roles_scope_map.length > 0) {
-                    const roleNames = ir.roles_scope_map.map(r => r.role_name).join(", ");
-                    process.stderr.write(`  ${ir.roles_scope_map.length} role scope(s) compiled: ${roleNames}\n`);
+        // Step 3.5: Plugin mode — write IR + register dna-hook
+        if (opts.plugin) {
+            const cwd = process.cwd();
+            // Write compiled IR
+            const dnas = await Promise.all(expandedFiles.map(loadDNA));
+            const cascadedForIR = cascadeDNA(dnas);
+            const roles = cascadedForIR.roles;
+            const compiled = createCompiledIR(ir, roles);
+            const irPath = await writeCompiledIR(cwd, compiled);
+            process.stderr.write(`Plugin: wrote ${irPath}\n`);
+            trackedOutputs.push(resolve(irPath));
+            // Register dna-hook events in settings.json
+            if (opts.settingsPath) {
+                const enabledEvents = detectEnabledEvents(ir);
+                if (enabledEvents.length > 0) {
+                    const pluginSettings = compilePluginSettings(enabledEvents);
+                    await mergeSettingsFile(pluginSettings, opts.settingsPath);
+                    process.stderr.write(`Plugin: registered ${enabledEvents.length} dna-hook event(s) in ${opts.settingsPath}\n`);
+                    trackedOutputs.push(resolve(opts.settingsPath));
                 }
             }
-            else {
-                process.stderr.write(`No hook-enforceable constraints found\n`);
+            // Clean up old bash hooks if they exist
+            const oldHooksDir = resolve(cwd, ".claude", "hooks");
+            const removed = await removeLegacyBashHooks(oldHooksDir);
+            if (removed > 0) {
+                process.stderr.write(`Plugin: cleaned ${removed} legacy bash hook(s) from ${oldHooksDir}\n`);
             }
         }
         // Step 5: Generate agent MD files
         if (opts.agentsDir) {
+            // Clean stale DNA-managed agents before regenerating
+            const staleAgents = await cleanStaleDNAFiles(opts.agentsDir, "agents");
+            if (staleAgents.length > 0) {
+                process.stderr.write(`Cleaned ${staleAgents.length} stale agent file(s)\n`);
+            }
             const dnas = await Promise.all(expandedFiles.map(loadDNA));
             const cascaded = cascadeDNA(dnas);
             const roles = cascaded.roles;
@@ -360,6 +431,11 @@ export async function runSync(opts) {
         }
         // Step 7: Generate skill files from workflows
         if (opts.skillsDir) {
+            // Clean stale DNA-managed skills before regenerating
+            const staleSkills = await cleanStaleDNAFiles(opts.skillsDir, "skills");
+            if (staleSkills.length > 0) {
+                process.stderr.write(`Cleaned ${staleSkills.length} stale skill dir(s)\n`);
+            }
             const dnas = await Promise.all(expandedFiles.map(loadDNA));
             const cascadedForSkills = cascadeDNA(dnas);
             const workflows = cascadedForSkills.workflows;
@@ -394,14 +470,6 @@ export async function runSync(opts) {
                 }
             }
         }
-        // Step 8: Generate/merge settings file
-        if (opts.settingsPath && opts.hooksDir) {
-            const hookScripts = compileToHooks(ir);
-            const dnaSettings = compileSettingsFromHooks(opts.hooksDir, hookScripts);
-            await mergeSettingsFile(dnaSettings, opts.settingsPath);
-            process.stderr.write(`Merged DNA hook config into ${opts.settingsPath}\n`);
-            trackedOutputs.push(resolve(opts.settingsPath));
-        }
         // Also output the compiled content to stderr for visibility
         const directiveCount = ir.prompt_directives.length;
         const gateCount = ir.pre_execution_gates.length;
@@ -420,4 +488,3 @@ export async function runSync(opts) {
         return 1;
     }
 }
-//# sourceMappingURL=sync.js.map

package/dist/cli/commands/validate.d.ts

@@ -8,4 +8,3 @@ export interface ValidateOptions {
     quiet: boolean;
 }
 export declare function runValidate(opts: ValidateOptions): Promise<number>;
-//# sourceMappingURL=validate.d.ts.map

package/dist/cli/commands/validate.js

@@ -27,4 +27,3 @@ export async function runValidate(opts) {
     }
     return allValid ? 0 : 1;
 }
-//# sourceMappingURL=validate.js.map

package/dist/cli/commands/verify.d.ts

@@ -30,4 +30,3 @@ export declare function sha256(content: string): string;
 export declare function parseLockFile(raw: string): LockFile;
 export declare function verifyLock(lock: LockFile): Promise<VerifyResult[]>;
 export declare function runVerify(opts: VerifyOptions): Promise<number>;
-//# sourceMappingURL=verify.d.ts.map

package/dist/cli/commands/verify.js

@@ -99,4 +99,3 @@ export async function runVerify(opts) {
         return 0;
     }
 }
-//# sourceMappingURL=verify.js.map

package/dist/cli/index.d.ts

@@ -12,4 +12,3 @@
  *   help       Show this help message
  */
 export {};
-//# sourceMappingURL=index.d.ts.map

package/dist/cli/index.js

@@ -87,6 +87,7 @@ async function main() {
                     settings: { type: "string" },
                     lock: { type: "string", default: ".dna/lock" },
                     remove: { type: "boolean", default: false },
+                    plugin: { type: "boolean", default: false },
                 },
                 allowPositionals: true,
                 strict: false,
@@ -108,6 +109,7 @@ async function main() {
                 settingsPath: values.settings,
                 lockFile: values.lock,
                 remove: values.remove,
+                plugin: values.plugin,
             });
             process.exit(code);
             break;
@@ -363,4 +365,3 @@ main().catch((err) => {
     process.stderr.write(`Fatal: ${err instanceof Error ? err.message : String(err)}\n`);
     process.exit(1);
 });
-//# sourceMappingURL=index.js.map

package/dist/cli/util/format.d.ts

@@ -21,4 +21,3 @@ export declare function formatCodon(codon: Codon): string;
  * Format a gene with its expression state for display.
  */
 export declare function formatGene(name: string, gene: ActivatedGene): string;
-//# sourceMappingURL=format.d.ts.map

package/dist/cli/util/format.js

@@ -64,4 +64,3 @@ export function formatGene(name, gene) {
     }
     return lines.join("\n");
 }
-//# sourceMappingURL=format.js.map

package/dist/cli/util/prompt.d.ts

@@ -8,4 +8,3 @@ export declare function askString(question: string, defaultVal?: string): Promis
 export declare function askNumber(question: string, defaultVal: number): Promise<number>;
 export declare function askChoice(question: string, choices: string[], defaultVal?: string): Promise<string>;
 export declare function askYesNo(question: string, defaultVal: boolean): Promise<boolean>;
-//# sourceMappingURL=prompt.d.ts.map

package/dist/cli/util/prompt.js

@@ -48,4 +48,3 @@ export async function askYesNo(question, defaultVal) {
         return defaultVal;
     return answer.toLowerCase().startsWith("y");
 }
-//# sourceMappingURL=prompt.js.map

package/dist/compiler/activate.d.ts

@@ -26,4 +26,3 @@ export interface ActivatedGene {
  * Returns the final gene expression state ready for compilation to IR.
  */
 export declare function activateDNA(cascaded: CascadedDNA, contextName?: string | null, activeRole?: string | null): ActivatedDNA;
-//# sourceMappingURL=activate.d.ts.map

package/dist/compiler/activate.js

@@ -138,4 +138,3 @@ export function activateDNA(cascaded, contextName = null, activeRole = null) {
         source_ids: cascaded.source_ids,
     };
 }
-//# sourceMappingURL=activate.js.map

package/dist/compiler/cascade.d.ts

@@ -10,12 +10,11 @@
  *   - attract/repel: same target accumulates, different targets independent
  *   - amplify/suppress: factors multiply (1.5x × 2.0x = 3.0x)
  */
-import type { IntentDNA, Gene, ContextRegion, EpigeneticMarker, RoleDef, WorkflowDef, ModeDef } from "../schema/types.js";
+import type { IntentDNA, Gene, ContextRegion, EpigeneticMarker, RoleDef, WorkflowDef } from "../schema/types.js";
 export interface CascadedDNA {
     genes: Record<string, Gene>;
     contexts: Record<string, ContextRegion>;
     roles: Record<string, RoleDef>;
-    modes: Record<string, ModeDef>;
     workflows: Record<string, WorkflowDef>;
     epigenetic_markers: EpigeneticMarker[];
     source_ids: string[];
@@ -31,4 +30,3 @@ export interface CascadedDNA {
  *   - Same namespace: higher priority replaces (expected cascade behavior)
  */
 export declare function cascadeDNA(layers: IntentDNA[]): CascadedDNA;
-//# sourceMappingURL=cascade.d.ts.map

package/dist/compiler/cascade.js

@@ -81,7 +81,6 @@ function prefixWorkflowRoles(wf, ns) {
         steps: wf.steps.map((step) => ({
             ...step,
             role: `${ns}_${step.role}`,
-            mode: step.mode ? `${ns}_${step.mode}` : undefined,
         })),
     };
 }
@@ -101,7 +100,6 @@ export function cascadeDNA(layers) {
     const mergedGenes = {};
     const mergedContexts = {};
     const mergedRoles = {};
-    const mergedModes = {};
     const mergedWorkflows = {};
     const allMarkers = [];
     const sourceIds = [];
@@ -126,12 +124,7 @@ export function cascadeDNA(layers) {
             const key = ns ? `${ns}_${name}` : name;
             mergedRoles[key] = role;
         }
-        // Merge modes: namespace-prefixed keys coexist, same-namespace overrides
-        for (const [name, mode] of Object.entries(dna.modes ?? {})) {
-            const key = ns ? `${ns}_${name}` : name;
-            mergedModes[key] = mode;
-        }
-        // Merge workflows: namespace-prefixed keys + step role/mode references
+        // Merge workflows: namespace-prefixed keys + step role references
         const normalized = normalizeWorkflowsFromDNA(dna);
         for (const [name, wf] of Object.entries(normalized)) {
             if (ns) {
@@ -151,10 +144,8 @@ export function cascadeDNA(layers) {
         genes: mergedGenes,
         contexts: mergedContexts,
         roles: mergedRoles,
-        modes: mergedModes,
         workflows: mergedWorkflows,
         epigenetic_markers: allMarkers,
         source_ids: sourceIds,
     };
 }
-//# sourceMappingURL=cascade.js.map

package/dist/compiler/compile.d.ts

@@ -14,4 +14,3 @@ import type { CascadedDNA } from "./cascade.js";
  * Compile activated DNA into a Constraint IR.
  */
 export declare function compileDNA(activated: ActivatedDNA, cascaded?: CascadedDNA): ConstraintIR;
-//# sourceMappingURL=compile.d.ts.map

package/dist/compiler/compile.js

@@ -198,26 +198,14 @@ export function compileDNA(activated, cascaded) {
             }
         }
     }
-    // Build mode_constraints from all cascaded modes
-    const modeConstraints = [];
-    if (cascaded?.modes) {
-        for (const [name, mode] of Object.entries(cascaded.modes)) {
-            modeConstraints.push({
-                mode_name: name,
-                description: mode.description,
-                tool_deny: mode.tool_permissions?.deny,
-                scope_write: mode.scope?.write,
-            });
-        }
-    }
-    // Build step_checkpoints from all workflow steps that have checkpoints + a mode
+    // Build step_checkpoints from all workflow steps that have checkpoints
     const stepCheckpoints = [];
     const allWorkflows = Object.values(cascaded?.workflows ?? {});
     for (const wf of allWorkflows) {
         for (const step of wf.steps ?? []) {
-            if (step.checkpoints && step.checkpoints.length > 0 && step.mode) {
+            if (step.checkpoints && step.checkpoints.length > 0) {
                 stepCheckpoints.push({
-                    step_mode: step.mode,
+                    step_role: step.role,
                     step_id: step.id,
                     checkpoints: [...step.checkpoints],
                 });
@@ -240,8 +228,6 @@ export function compileDNA(activated, cascaded) {
         role_tool_permissions: roleToolPermissions,
         role_scope: roleScope,
         roles_scope_map: rolesScopeMap.length > 0 ? rolesScopeMap : undefined,
-        mode_constraints: modeConstraints.length > 0 ? modeConstraints : undefined,
         step_checkpoints: stepCheckpoints.length > 0 ? stepCheckpoints : undefined,
     };
 }
-//# sourceMappingURL=compile.js.map

package/dist/compiler/index.d.ts

@@ -25,4 +25,3 @@ export interface CompileOptions {
  * Optionally injects stored epigenetic markers from the evolution engine.
  */
 export declare function compileFromFiles(filePaths: string[], contextOrOptions?: string | CompileOptions): Promise<ConstraintIR>;
-//# sourceMappingURL=index.d.ts.map

package/dist/compiler/index.js

@@ -48,4 +48,3 @@ export async function compileFromFiles(filePaths, contextOrOptions) {
     const activated = activateDNA(cascaded, opts.context ?? null, opts.role ?? null);
     return compileDNA(activated, cascaded);
 }
-//# sourceMappingURL=index.js.map

package/dist/compiler/workflow.d.ts

@@ -34,4 +34,3 @@ export interface CompileWorkflowResult {
  * Returns a result object with either a plan or errors.
  */
 export declare function compileWorkflow(workflow: WorkflowDef, options?: CompileWorkflowOptions): CompileWorkflowResult;
-//# sourceMappingURL=workflow.d.ts.map

package/dist/compiler/workflow.js

@@ -166,7 +166,6 @@ function toWorkflowStep(def) {
     return {
         id: def.id,
         role: def.role,
-        mode: def.mode ?? null,
         description: def.description ?? def.id,
         optional: def.optional ?? false,
         run_if: resolveRunIf(def.run_if),
@@ -273,4 +272,3 @@ export function compileWorkflow(workflow, options) {
     }
     return { ok: true, plan, errors: [] };
 }
-//# sourceMappingURL=workflow.js.map

package/dist/evolution/collector.d.ts

@@ -49,4 +49,3 @@ export interface OutcomeSummary {
     oldest: string | null;
     newest: string | null;
 }
-//# sourceMappingURL=collector.d.ts.map

package/dist/evolution/collector.js

@@ -69,4 +69,3 @@ export class OutcomeCollector {
         };
     }
 }
-//# sourceMappingURL=collector.js.map