intentdna 1.0.0

package/dist/cli/index.d.ts

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+#!/usr/bin/env node
+/**
+ * Intent DNA — CLI Entry Point
+ *
+ * Usage: dna <command> [options]
+ *
+ * Commands:
+ *   init       Create a new DNA file interactively
+ *   compile    Compile DNA files to framework configuration
+ *   validate   Validate DNA files
+ *   show       Show gene expression state
+ *   help       Show this help message
+ */
+export {};
+//# sourceMappingURL=index.d.ts.map

package/dist/cli/index.d.ts.map

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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/cli/index.ts"],"names":[],"mappings":";AAEA;;;;;;;;;;;GAWG"}

package/dist/cli/index.js

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+#!/usr/bin/env node
+/**
+ * Intent DNA — CLI Entry Point
+ *
+ * Usage: dna <command> [options]
+ *
+ * Commands:
+ *   init       Create a new DNA file interactively
+ *   compile    Compile DNA files to framework configuration
+ *   validate   Validate DNA files
+ *   show       Show gene expression state
+ *   help       Show this help message
+ */
+import { parseArgs } from "node:util";
+const HELP = `Intent DNA CLI v0.3.0
+
+Usage: dna <command> [options]
+
+Commands:
+  guard         Zero-config guardrails — detect environment, apply safety rules
+  sync          Compile + inject DNA into target file (CLAUDE.md, SOUL.md, etc.)
+  verify        Verify synced files match .dna.lock checksums (drift detection)
+  run           Execute a workflow directly (TypeScript runtime)
+  init          Create a new DNA file interactively
+  compile       Compile DNA files to framework configuration
+  validate      Validate DNA files for correctness
+  show          Show gene expression state
+  evolve        Generate epigenetic markers from outcomes
+  epigenetic    Record outcomes, view markers and summaries
+
+Options:
+  --help, -h    Show help for a command
+
+Examples:
+  dna guard                           Apply standard guardrails (auto-detect environment)
+  dna guard --level yolo              YOLO mode with safety net
+  dna guard --level strict            Enterprise-grade guardrails
+  dna guard --audit                   Show last 7 days of violation logs
+  dna guard --remove                  Remove all guardrails
+  dna sync my.dna.json --target claude-md --inject CLAUDE.md --context work
+  dna sync my.dna.json --target claude-md --inject CLAUDE.md --hooks .claude/hooks
+  dna sync my.dna.json --hooks .claude/hooks --context work
+  dna sync my.dna.json --hooks .claude/hooks --role reviewer
+  dna sync my.dna.json --agents .claude/agents
+  dna sync my.dna.json --workflow ./scripts
+  dna sync my.dna.json --target claude-md --inject CLAUDE.md --hooks .claude/hooks --agents .claude/agents --workflow ./scripts
+  dna sync my.dna.json --target soul-md --inject SOUL.md --evolve
+  dna sync --remove --inject CLAUDE.md --hooks .claude/hooks --agents .claude/agents
+  dna verify                          Verify synced files against .dna.lock
+  dna verify --lock /path/to/.dna.lock
+  dna import .                  Import existing harness configs into DNA format
+  dna run --dna my.dna.json --workflow dev-pipeline --task P5.8
+  dna run --dna my.dna.json --workflow dev-pipeline --task P5.8 --dry-run
+  dna compile my.dna.json --context work
+  dna show my.dna.json --context work
+  dna evolve my_dna_id --preview
+`;
+async function main() {
+    const args = process.argv.slice(2);
+    const command = args[0];
+    if (!command || command === "help" || command === "--help" || command === "-h") {
+        process.stderr.write(HELP);
+        process.exit(0);
+    }
+    // Parse remaining args (after command)
+    const rest = args.slice(1);
+    switch (command) {
+        case "sync": {
+            const { values, positionals } = parseArgs({
+                args: rest,
+                options: {
+                    target: { type: "string", short: "t", default: "claude-md" },
+                    inject: { type: "string", short: "i" },
+                    context: { type: "string", short: "c" },
+                    role: { type: "string", short: "r" },
+                    evolve: { type: "boolean", default: false },
+                    "store-dir": { type: "string" },
+                    hooks: { type: "string" },
+                    agents: { type: "string" },
+                    workflow: { type: "string" },
+                    "workflow-name": { type: "string" },
+                    skills: { type: "string" },
+                    settings: { type: "string" },
+                    lock: { type: "string", default: ".dna.lock" },
+                    remove: { type: "boolean", default: false },
+                },
+                allowPositionals: true,
+                strict: false,
+            });
+            const { runSync } = await import("./commands/sync.js");
+            const code = await runSync({
+                files: positionals,
+                target: values.target,
+                inject: values.inject,
+                context: values.context,
+                role: values.role,
+                evolve: values.evolve,
+                storeDir: values["store-dir"],
+                hooksDir: values.hooks,
+                agentsDir: values.agents,
+                workflowDir: values.workflow,
+                workflowName: values["workflow-name"],
+                skillsDir: values.skills,
+                settingsPath: values.settings,
+                lockFile: values.lock,
+                remove: values.remove,
+            });
+            process.exit(code);
+            break;
+        }
+        case "verify": {
+            const { values: verifyValues } = parseArgs({
+                args: rest,
+                options: {
+                    lock: { type: "string", default: ".dna.lock" },
+                },
+                allowPositionals: true,
+                strict: false,
+            });
+            const { runVerify } = await import("./commands/verify.js");
+            const code = await runVerify({
+                lockFile: verifyValues.lock,
+            });
+            process.exit(code);
+            break;
+        }
+        case "run": {
+            const { values: runValues, positionals: runPositionals } = parseArgs({
+                args: rest,
+                options: {
+                    dna: { type: "string", multiple: true },
+                    workflow: { type: "string", short: "w" },
+                    task: { type: "string", short: "t" },
+                    context: { type: "string", short: "c" },
+                    var: { type: "string", multiple: true },
+                    "dry-run": { type: "boolean", default: false },
+                    "max-budget": { type: "string" },
+                    "log-dir": { type: "string" },
+                    "permission-mode": { type: "string" },
+                    agents: { type: "string" },
+                    hooks: { type: "string" },
+                },
+                allowPositionals: true,
+                strict: false,
+            });
+            // Parse --var key=value pairs
+            const varEntries = runValues.var ?? [];
+            const vars = {};
+            for (const v of varEntries) {
+                const eqIdx = v.indexOf("=");
+                if (eqIdx > 0) {
+                    vars[v.slice(0, eqIdx)] = v.slice(eqIdx + 1);
+                }
+            }
+            const { runRun } = await import("./commands/run.js");
+            const code = await runRun({
+                dnaFiles: runValues.dna ?? runPositionals,
+                workflowName: runValues.workflow,
+                taskId: runValues.task,
+                context: runValues.context,
+                vars: Object.keys(vars).length > 0 ? vars : undefined,
+                dryRun: runValues["dry-run"],
+                maxBudget: runValues["max-budget"]
+                    ? parseFloat(runValues["max-budget"])
+                    : undefined,
+                logDir: runValues["log-dir"],
+                permissionMode: runValues["permission-mode"],
+                agentsDir: runValues.agents,
+                hooksDir: runValues.hooks,
+            });
+            process.exit(code);
+            break;
+        }
+        case "import": {
+            const { values: importValues, positionals: importPositionals } = parseArgs({
+                args: rest,
+                options: {
+                    output: { type: "string", short: "o" },
+                    format: { type: "string", short: "f", default: "yaml" },
+                },
+                allowPositionals: true,
+                strict: false,
+            });
+            const { runImport } = await import("./commands/import.js");
+            const code = await runImport({
+                dir: importPositionals[0] ?? ".",
+                output: importValues.output,
+                format: importValues.format ?? "yaml",
+            });
+            process.exit(code);
+            break;
+        }
+        case "validate": {
+            const { values, positionals } = parseArgs({
+                args: rest,
+                options: {
+                    quiet: { type: "boolean", short: "q", default: false },
+                },
+                allowPositionals: true,
+                strict: false,
+            });
+            const { runValidate } = await import("./commands/validate.js");
+            const code = await runValidate({
+                files: positionals,
+                quiet: values.quiet,
+            });
+            process.exit(code);
+            break;
+        }
+        case "compile": {
+            const { values, positionals } = parseArgs({
+                args: rest,
+                options: {
+                    target: { type: "string", short: "t", default: "claude-sdk" },
+                    context: { type: "string", short: "c" },
+                    output: { type: "string", short: "o" },
+                    ir: { type: "boolean", default: false },
+                },
+                allowPositionals: true,
+                strict: false,
+            });
+            const { runCompile } = await import("./commands/compile.js");
+            const code = await runCompile({
+                files: positionals,
+                target: values.target,
+                context: values.context,
+                output: values.output,
+                ir: values.ir,
+            });
+            process.exit(code);
+            break;
+        }
+        case "show": {
+            const { values, positionals } = parseArgs({
+                args: rest,
+                options: {
+                    context: { type: "string", short: "c" },
+                    json: { type: "boolean", default: false },
+                },
+                allowPositionals: true,
+                strict: false,
+            });
+            const { runShow } = await import("./commands/show.js");
+            const code = await runShow({
+                files: positionals,
+                context: values.context,
+                json: values.json,
+            });
+            process.exit(code);
+            break;
+        }
+        case "init": {
+            const { values } = parseArgs({
+                args: rest,
+                options: {
+                    type: { type: "string", short: "t" },
+                    name: { type: "string", short: "n" },
+                    output: { type: "string", short: "o" },
+                    template: { type: "string" },
+                },
+                allowPositionals: true,
+                strict: false,
+            });
+            const { runInit } = await import("./commands/init.js");
+            const code = await runInit({
+                type: values.type,
+                name: values.name,
+                output: values.output,
+                template: values.template,
+            });
+            process.exit(code);
+            break;
+        }
+        case "evolve": {
+            const { values, positionals } = parseArgs({
+                args: rest,
+                options: {
+                    preview: { type: "boolean", default: false },
+                    "store-dir": { type: "string" },
+                },
+                allowPositionals: true,
+                strict: false,
+            });
+            const { runEvolve } = await import("./commands/evolve.js");
+            const code = await runEvolve({
+                dnaId: positionals[0] ?? "",
+                preview: values.preview,
+                storeDir: values["store-dir"],
+            });
+            process.exit(code);
+            break;
+        }
+        case "epigenetic": {
+            const subcommand = rest[0] ?? "";
+            const epiRest = rest.slice(1);
+            const { values: epiValues, positionals: epiPositionals } = parseArgs({
+                args: epiRest,
+                options: {
+                    "store-dir": { type: "string" },
+                    action: { type: "string" },
+                    success: { type: "boolean", default: true },
+                    genes: { type: "string" },
+                    feedback: { type: "string" },
+                    json: { type: "boolean", default: false },
+                },
+                allowPositionals: true,
+                strict: false,
+            });
+            const { runEpigenetic } = await import("./commands/epigenetic.js");
+            const genesStr = epiValues.genes;
+            const code = await runEpigenetic({
+                subcommand,
+                dnaId: epiPositionals[0] ?? "",
+                storeDir: epiValues["store-dir"],
+                action: epiValues.action,
+                success: epiValues.success,
+                genes: genesStr ? genesStr.split(",") : undefined,
+                feedback: epiValues.feedback,
+                json: epiValues.json,
+            });
+            process.exit(code);
+            break;
+        }
+        case "guard": {
+            const { values: guardValues } = parseArgs({
+                args: rest,
+                options: {
+                    level: { type: "string", short: "l", default: "standard" },
+                    audit: { type: "boolean", default: false },
+                    remove: { type: "boolean", default: false },
+                },
+                strict: false,
+            });
+            const { runGuard } = await import("./commands/guard.js");
+            const guardLevel = guardValues.level;
+            if (!["standard", "yolo", "strict"].includes(guardLevel)) {
+                process.stderr.write(`Error: unknown level '${guardLevel}'. Available: standard, yolo, strict\n`);
+                process.exit(2);
+            }
+            const code = await runGuard({
+                level: guardLevel,
+                audit: guardValues.audit,
+                remove: guardValues.remove,
+            });
+            process.exit(code);
+            break;
+        }
+        default:
+            process.stderr.write(`Unknown command: ${command}\n\n`);
+            process.stderr.write(HELP);
+            process.exit(2);
+    }
+}
+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/index.js.map

@@ -0,0 +1 @@
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package/dist/cli/util/format.d.ts

@@ -0,0 +1,24 @@
+/**
+ * Intent DNA — CLI Terminal Formatting Utilities
+ */
+import type { ActivatedGene } from "../../compiler/activate.js";
+import type { Codon } from "../../schema/types.js";
+export declare function bold(s: string): string;
+export declare function dim(s: string): string;
+export declare function green(s: string): string;
+export declare function yellow(s: string): string;
+export declare function red(s: string): string;
+export declare function cyan(s: string): string;
+/**
+ * Map expression level to a human-readable label with color.
+ */
+export declare function expressionLabel(level: number): string;
+/**
+ * Format a single codon for display.
+ */
+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.d.ts.map

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package/dist/cli/util/format.js

@@ -0,0 +1,67 @@
+/**
+ * Intent DNA — CLI Terminal Formatting Utilities
+ */
+const BOLD = "\x1b[1m";
+const DIM = "\x1b[2m";
+const RESET = "\x1b[0m";
+const GREEN = "\x1b[32m";
+const YELLOW = "\x1b[33m";
+const RED = "\x1b[31m";
+const CYAN = "\x1b[36m";
+export function bold(s) { return `${BOLD}${s}${RESET}`; }
+export function dim(s) { return `${DIM}${s}${RESET}`; }
+export function green(s) { return `${GREEN}${s}${RESET}`; }
+export function yellow(s) { return `${YELLOW}${s}${RESET}`; }
+export function red(s) { return `${RED}${s}${RESET}`; }
+export function cyan(s) { return `${CYAN}${s}${RESET}`; }
+/**
+ * Map expression level to a human-readable label with color.
+ */
+export function expressionLabel(level) {
+    if (level === 0)
+        return dim("OFF");
+    if (level >= 2.0)
+        return red("VERY HIGH");
+    if (level >= 1.5)
+        return yellow("HIGH");
+    if (level >= 1.0)
+        return green("NORMAL");
+    if (level >= 0.5)
+        return dim("LOW");
+    return dim("VERY LOW");
+}
+/**
+ * Format a single codon for display.
+ */
+export function formatCodon(codon) {
+    switch (codon.type) {
+        case "attract":
+            return `  + attract ${cyan(codon.target)}`;
+        case "repel":
+            return `  - repel   ${cyan(codon.target)}`;
+        case "threshold":
+            return `  ! threshold ${cyan(codon.condition)}`;
+        case "weight":
+            return `  ~ weight  ${cyan(codon.a)}(${Math.round(codon.ratio * 100)}%) vs ${cyan(codon.b)}(${Math.round((1 - codon.ratio) * 100)}%)`;
+        case "sense":
+            return `  ? sense   ${cyan(codon.signal)} -> ${codon.response}`;
+    }
+}
+/**
+ * Format a gene with its expression state for display.
+ */
+export function formatGene(name, gene) {
+    const lines = [];
+    const label = expressionLabel(gene.expression_level);
+    const levelStr = gene.expression_level.toFixed(2);
+    lines.push(`${bold(name)} ${dim(`(${levelStr})`)} ${label}`);
+    lines.push(`  ${dim(gene.description)}`);
+    for (const codon of gene.codons) {
+        lines.push(formatCodon(codon));
+    }
+    if (gene.tags.length > 0) {
+        lines.push(`  ${dim(`tags: ${gene.tags.join(", ")}`)}`);
+    }
+    return lines.join("\n");
+}
+//# sourceMappingURL=format.js.map

package/dist/cli/util/format.js.map

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

@@ -0,0 +1,11 @@
+/**
+ * Intent DNA — CLI Interactive Prompt Utilities
+ *
+ * Wraps node:readline/promises for simple interactive input.
+ */
+export declare function closePrompt(): void;
+export declare function askString(question: string, defaultVal?: string): Promise<string>;
+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.d.ts.map

@@ -0,0 +1 @@
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package/dist/cli/util/prompt.js

@@ -0,0 +1,51 @@
+/**
+ * Intent DNA — CLI Interactive Prompt Utilities
+ *
+ * Wraps node:readline/promises for simple interactive input.
+ */
+import { createInterface } from "node:readline/promises";
+import { stdin, stderr } from "node:process";
+let rl = null;
+function getRL() {
+    if (!rl) {
+        rl = createInterface({ input: stdin, output: stderr });
+    }
+    return rl;
+}
+export function closePrompt() {
+    if (rl) {
+        rl.close();
+        rl = null;
+    }
+}
+export async function askString(question, defaultVal) {
+    const suffix = defaultVal ? ` [${defaultVal}]` : "";
+    const answer = await getRL().question(`${question}${suffix}: `);
+    return answer.trim() || defaultVal || "";
+}
+export async function askNumber(question, defaultVal) {
+    const answer = await askString(question, String(defaultVal));
+    const num = Number(answer);
+    return isNaN(num) ? defaultVal : num;
+}
+export async function askChoice(question, choices, defaultVal) {
+    const choiceStr = choices
+        .map((c, i) => `  ${i + 1}) ${c}${c === defaultVal ? " (default)" : ""}`)
+        .join("\n");
+    stderr.write(`${question}\n${choiceStr}\n`);
+    const answer = await askString("Choose");
+    const num = Number(answer);
+    if (num >= 1 && num <= choices.length)
+        return choices[num - 1];
+    if (choices.includes(answer))
+        return answer;
+    return defaultVal || choices[0];
+}
+export async function askYesNo(question, defaultVal) {
+    const suffix = defaultVal ? "[Y/n]" : "[y/N]";
+    const answer = await askString(`${question} ${suffix}`);
+    if (!answer)
+        return defaultVal;
+    return answer.toLowerCase().startsWith("y");
+}
+//# sourceMappingURL=prompt.js.map

package/dist/cli/util/prompt.js.map

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package/dist/compiler/activate.d.ts

@@ -0,0 +1,29 @@
+/**
+ * Intent DNA — Context Activator
+ *
+ * Given a cascaded DNA and an active context name, applies Regulatory Regions:
+ *   - amplify/suppress gene codons by factor
+ *   - activate/deactivate genes
+ *   - apply threshold overrides
+ *   - apply epigenetic markers with decay
+ */
+import type { Codon } from "../schema/types.js";
+import type { CascadedDNA } from "./cascade.js";
+export interface ActivatedDNA {
+    genes: Record<string, ActivatedGene>;
+    active_context: string | null;
+    active_role: string | null;
+    source_ids: string[];
+}
+export interface ActivatedGene {
+    description: string;
+    codons: Codon[];
+    tags: string[];
+    expression_level: number;
+}
+/**
+ * Activate a cascaded DNA for a given context and role.
+ * 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.d.ts.map

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