contextos-mcp 0.4.0

package/dist/worktree/merge.d.ts

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+/**
+ * Merge thread branches back into the main branch.
+ *
+ * Phase 2 enhancements:
+ *   - Partial merge: continues merging non-conflicting branches after a conflict
+ *   - Conflict hunks: captures the actual diff of conflicted files
+ *   - Merge ordering: accepts optional order array from orchestrator
+ */
+import type { MergeResult, ThreadState } from "../core/types.js";
+export interface MergeEligibility {
+    eligible: boolean;
+    reason?: string;
+}
+export interface MergeEligibilityOptions {
+    currentHeadSha?: string;
+    currentDiffSha256?: string;
+    repositoryFingerprint?: string;
+    isAutoMerge?: boolean;
+    userOverride?: boolean;
+    isFromRepoConfig?: boolean;
+}
+/**
+ * Strict merge predicate:
+ * A thread is eligible for merge if and only if:
+ * 1. Status is "completed"
+ * 2. Result exists and success is true
+ * 3. Scope violation flag is false/absent
+ * 4. Automated verification attestation passed ("PASS") with valid proof-of-work evidence
+ * 5. Independent review attestation passed ("PASS") with rawOutputDigest and dual PASS verdicts
+ * 6. Attestation subjects match each other and bind to exact candidate state (headSha, diffSha256, repositoryFingerprint)
+ * 7. Candidate state has not diverged from attestation subjects (otherwise marks attestations STALE)
+ */
+export declare function isEligibleForMerge(thread: ThreadState, options?: MergeEligibilityOptions): MergeEligibility;
+/**
+ * Merge a single thread branch into the current branch.
+ * On conflict, captures the conflicted file list and diff hunks before aborting.
+ */
+export declare function mergeThreadBranch(repoRoot: string, branchName: string, threadId: string, threadState?: ThreadState): Promise<MergeResult>;
+export interface MergeAllOptions {
+    /** Explicit merge order — thread IDs in desired merge sequence. */
+    order?: string[];
+    /** If true, continue merging remaining branches after a conflict (default: true). */
+    continueOnConflict?: boolean;
+    /** If true, user-local safety override to allow host-unsafe auto-merge. */
+    userOverride?: boolean;
+    /** If true, indicates the override originated from repo-scoped config (strictly rejected). */
+    isFromRepoConfig?: boolean;
+    /** Whether this is an auto-merge batch invocation (defaults to false for backwards-compatibility). */
+    isAutoMerge?: boolean;
+}
+/**
+ * Merge all completed thread branches sequentially.
+ *
+ * Supports:
+ *   - Custom merge order via options.order
+ *   - Partial merge: by default continues past conflicts (skips conflicting branch)
+ */
+export declare function mergeAllThreads(repoRoot: string, threads: ThreadState[], options?: MergeAllOptions): Promise<MergeResult[]>;

package/dist/worktree/merge.js

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+/**
+ * Merge thread branches back into the main branch.
+ *
+ * Phase 2 enhancements:
+ *   - Partial merge: continues merging non-conflicting branches after a conflict
+ *   - Conflict hunks: captures the actual diff of conflicted files
+ *   - Merge ordering: accepts optional order array from orchestrator
+ */
+import { execFile } from "node:child_process";
+import { createHash } from "node:crypto";
+import * as path from "node:path";
+import { assertWithinRepository, SecurityBoundaryException } from "../security/repository-boundary.js";
+import { createRepositoryFingerprint } from "./manager.js";
+function git(args, cwd) {
+    return new Promise((resolve, reject) => {
+        execFile("git", args, { cwd, maxBuffer: 10 * 1024 * 1024 }, (err, stdout, stderr) => {
+            if (err) {
+                // Include stdout in error message — git merge writes CONFLICT info to stdout
+                const detail = [stderr, stdout].filter((s) => s?.trim()).join("\n") || err.message;
+                reject(new Error(`git ${args[0]} failed: ${detail}`));
+            }
+            else {
+                resolve({ stdout, stderr });
+            }
+        });
+    });
+}
+/** Abort a merge safely without ever destroying user's uncommitted work tree. */
+async function abortMergeSafe(repoRoot) {
+    try {
+        await git(["merge", "--abort"], repoRoot);
+    }
+    catch {
+        // NEVER run git reset --hard HEAD in repoRoot: it would erase user's uncommitted files.
+        // If git merge --abort failed, leave the workspace intact for manual inspection.
+    }
+}
+/**
+ * Strict merge predicate:
+ * A thread is eligible for merge if and only if:
+ * 1. Status is "completed"
+ * 2. Result exists and success is true
+ * 3. Scope violation flag is false/absent
+ * 4. Automated verification attestation passed ("PASS") with valid proof-of-work evidence
+ * 5. Independent review attestation passed ("PASS") with rawOutputDigest and dual PASS verdicts
+ * 6. Attestation subjects match each other and bind to exact candidate state (headSha, diffSha256, repositoryFingerprint)
+ * 7. Candidate state has not diverged from attestation subjects (otherwise marks attestations STALE)
+ */
+export function isEligibleForMerge(thread, options) {
+    if (thread.status !== "completed") {
+        return { eligible: false, reason: `Thread status is "${thread.status}", expected "completed"` };
+    }
+    if (!thread.result?.success) {
+        return { eligible: false, reason: "Thread execution result is not successful" };
+    }
+    if (thread.scopeViolation) {
+        return { eligible: false, reason: "Thread touched files outside its assigned writeScope" };
+    }
+    // 1. Verification Attestation validation
+    if (!thread.verificationAttestation) {
+        return {
+            eligible: false,
+            reason: "Missing verification attestation",
+        };
+    }
+    const vAtt = thread.verificationAttestation;
+    // Invalidation to STALE if live candidate options provided and mismatched
+    if (options?.currentHeadSha && vAtt.subject?.headSha && vAtt.subject.headSha !== options.currentHeadSha) {
+        vAtt.status = "STALE";
+        if (thread.reviewAttestation)
+            thread.reviewAttestation.status = "STALE";
+        thread.verificationStatus = "STALE";
+        thread.reviewStatus = "STALE";
+        thread.mergeStatus = "BLOCKED";
+        return {
+            eligible: false,
+            reason: `Candidate branch HEAD commit (${options.currentHeadSha}) does not match verification subject headSha (${vAtt.subject.headSha}): attestation is STALE`,
+        };
+    }
+    if (options?.currentDiffSha256 && vAtt.subject?.diffSha256 && vAtt.subject.diffSha256 !== options.currentDiffSha256) {
+        vAtt.status = "STALE";
+        if (thread.reviewAttestation)
+            thread.reviewAttestation.status = "STALE";
+        thread.verificationStatus = "STALE";
+        thread.reviewStatus = "STALE";
+        thread.mergeStatus = "BLOCKED";
+        return {
+            eligible: false,
+            reason: `Candidate diff hash (${options.currentDiffSha256}) does not match verification subject diffSha256 (${vAtt.subject.diffSha256}): attestation is STALE`,
+        };
+    }
+    if (options?.repositoryFingerprint &&
+        vAtt.subject?.repositoryFingerprint &&
+        vAtt.subject.repositoryFingerprint !== options.repositoryFingerprint) {
+        return {
+            eligible: false,
+            reason: `Repository fingerprint mismatch: attestation is for "${vAtt.subject.repositoryFingerprint}", repository is "${options.repositoryFingerprint}"`,
+        };
+    }
+    // Negative status matrix check for verification
+    if (vAtt.status !== "PASS") {
+        const detail = vAtt.status === "NOT_CONFIGURED"
+            ? "evidence-bearing PASS required"
+            : vAtt.status === "STALE"
+                ? "candidate changed after verification"
+                : vAtt.status === "UNAVAILABLE"
+                    ? "verifier service unavailable"
+                    : vAtt.status === "MALFORMED"
+                        ? "verifier output malformed"
+                        : vAtt.status;
+        return {
+            eligible: false,
+            reason: `Verification status is not PASS. Status is "${vAtt.status}" (${detail})`,
+        };
+    }
+    // Verification Evidence verification (evidence-bearing PASS)
+    if (!vAtt.evidence) {
+        return {
+            eligible: false,
+            reason: "Verification attestation is missing proof-of-work evidence",
+        };
+    }
+    if (vAtt.subject?.headSha && (!vAtt.evidence.outputSha256 || !vAtt.evidence.outputSha256.trim())) {
+        return {
+            eligible: false,
+            reason: "Verification attestation is missing proof-of-work evidence: outputSha256 digest required",
+        };
+    }
+    // Host-unsafe auto-merge governance (Section 19.1 & W5.4)
+    if (options?.isAutoMerge && vAtt.runnerMode === "host-unsafe") {
+        if (options.userOverride) {
+            if (options.isFromRepoConfig) {
+                return {
+                    eligible: false,
+                    reason: "Auto-merge blocked: repository configuration cannot enable host-unsafe auto-merge override. Only user-local safety override is permitted.",
+                };
+            }
+        }
+        else {
+            return {
+                eligible: false,
+                reason: "Auto-merge blocked: candidate was verified in host-unsafe mode. Isolated OCI container or explicit user-local safety override required.",
+            };
+        }
+    }
+    // 2. Review Attestation validation
+    if (!thread.reviewAttestation) {
+        return {
+            eligible: false,
+            reason: "Missing review attestation: rejected by independent reviewer gate",
+        };
+    }
+    const rAtt = thread.reviewAttestation;
+    // Invalidation to STALE if live candidate options provided and mismatched
+    if (options?.currentHeadSha && rAtt.subject?.headSha && rAtt.subject.headSha !== options.currentHeadSha) {
+        rAtt.status = "STALE";
+        thread.reviewStatus = "STALE";
+        thread.mergeStatus = "BLOCKED";
+        return {
+            eligible: false,
+            reason: `Candidate branch HEAD commit (${options.currentHeadSha}) does not match review subject headSha (${rAtt.subject.headSha}): attestation is STALE`,
+        };
+    }
+    if (options?.currentDiffSha256 && rAtt.subject?.diffSha256 && rAtt.subject.diffSha256 !== options.currentDiffSha256) {
+        rAtt.status = "STALE";
+        thread.reviewStatus = "STALE";
+        thread.mergeStatus = "BLOCKED";
+        return {
+            eligible: false,
+            reason: `Candidate diff hash (${options.currentDiffSha256}) does not match review subject diffSha256 (${rAtt.subject.diffSha256}): attestation is STALE`,
+        };
+    }
+    // Negative status matrix check for review
+    if (rAtt.status !== "PASS") {
+        const detail = rAtt.status === "NOT_CONFIGURED"
+            ? "evidence-bearing PASS required"
+            : rAtt.status === "STALE"
+                ? "candidate changed after review"
+                : rAtt.status === "UNAVAILABLE"
+                    ? "reviewer service unavailable"
+                    : rAtt.status === "MALFORMED"
+                        ? "reviewer output malformed"
+                        : rAtt.status;
+        return {
+            eligible: false,
+            reason: `Review status is not PASS. Status is "${rAtt.status}" (${detail})`,
+        };
+    }
+    // Review Evidence verification (rawOutputDigest required)
+    if (rAtt.subject?.headSha && (!rAtt.rawOutputDigest || !rAtt.rawOutputDigest.trim())) {
+        return {
+            eligible: false,
+            reason: "Review attestation is missing evidence: rawOutputDigest digest required",
+        };
+    }
+    // Dual-verdict checks
+    if (rAtt.llmVerdict?.specCompliance !== "PASS") {
+        return {
+            eligible: false,
+            reason: `Review failed: specCompliance is ${rAtt.llmVerdict?.specCompliance || "MISSING"}. Summary: ${rAtt.llmVerdict?.summary}`,
+        };
+    }
+    if (rAtt.llmVerdict?.codeQuality !== "PASS") {
+        return {
+            eligible: false,
+            reason: `Review failed: codeQuality is ${rAtt.llmVerdict?.codeQuality || "MISSING"}. Summary: ${rAtt.llmVerdict?.summary}`,
+        };
+    }
+    // 3. Subject Completeness and Cross-Attestation Binding
+    const vSub = vAtt.subject;
+    const rSub = rAtt.subject;
+    if (!vSub || !rSub) {
+        return { eligible: false, reason: "Missing attestation subject" };
+    }
+    // Cross-attestation consistency
+    if (vSub.headSha && rSub.headSha && vSub.headSha !== rSub.headSha) {
+        return {
+            eligible: false,
+            reason: `Subject headSha mismatch between verification ("${vSub.headSha}") and review ("${rSub.headSha}") attestations`,
+        };
+    }
+    if (vSub.diffSha256 && rSub.diffSha256 && vSub.diffSha256 !== rSub.diffSha256) {
+        return {
+            eligible: false,
+            reason: `Subject diffSha256 mismatch between verification ("${vSub.diffSha256}") and review ("${rSub.diffSha256}") attestations`,
+        };
+    }
+    if (vSub.repositoryFingerprint &&
+        rSub.repositoryFingerprint &&
+        vSub.repositoryFingerprint !== rSub.repositoryFingerprint) {
+        return {
+            eligible: false,
+            reason: `Subject repositoryFingerprint mismatch between verification ("${vSub.repositoryFingerprint}") and review ("${rSub.repositoryFingerprint}") attestations`,
+        };
+    }
+    if (vSub.baseSha && rSub.baseSha && vSub.baseSha !== rSub.baseSha) {
+        return {
+            eligible: false,
+            reason: `Subject baseSha mismatch between verification ("${vSub.baseSha}") and review ("${rSub.baseSha}") attestations`,
+        };
+    }
+    return { eligible: true };
+}
+/**
+ * Merge a single thread branch into the current branch.
+ * On conflict, captures the conflicted file list and diff hunks before aborting.
+ */
+export async function mergeThreadBranch(repoRoot, branchName, threadId, threadState) {
+    const canonicalRepoRoot = assertWithinRepository(repoRoot, repoRoot);
+    if (!branchName || branchName.startsWith("-") || branchName.includes("..") || path.isAbsolute(branchName)) {
+        throw new SecurityBoundaryException(`Invalid branch name: ${branchName}`);
+    }
+    assertWithinRepository(path.resolve(canonicalRepoRoot, ".git", "refs", "heads", branchName), canonicalRepoRoot);
+    if (threadState) {
+        let currentHeadSha;
+        let currentDiffSha256;
+        try {
+            const { stdout: headOut } = await git(["rev-parse", branchName], canonicalRepoRoot);
+            currentHeadSha = headOut.trim();
+            const baseSha = threadState.verificationAttestation?.subject?.baseSha || threadState.taskBrief?.baseSha;
+            if (baseSha) {
+                const { stdout: diffOut } = await git(["diff", `${baseSha}...${branchName}`, "--", ":(exclude).contextos-owner", ":(exclude).contextos-session"], canonicalRepoRoot);
+                currentDiffSha256 = createHash("sha256").update(diffOut).digest("hex");
+            }
+        }
+        catch {
+            // Branch query failure will be surfaced either by predicate or git merge
+        }
+        const repoFingerprint = createRepositoryFingerprint(canonicalRepoRoot);
+        const check = isEligibleForMerge(threadState, {
+            currentHeadSha,
+            currentDiffSha256,
+            repositoryFingerprint: repoFingerprint,
+        });
+        if (!check.eligible) {
+            return {
+                success: false,
+                branch: branchName,
+                conflicts: [],
+                conflictDiff: "",
+                message: `Merge blocked by strict merge predicate: ${check.reason}`,
+            };
+        }
+    }
+    try {
+        const { stdout } = await git(["merge", "--no-ff", "-m", `swarm: merge thread ${threadId}`, branchName], canonicalRepoRoot);
+        if (threadState) {
+            threadState.mergeStatus = "MERGED";
+        }
+        return {
+            success: true,
+            branch: branchName,
+            conflicts: [],
+            conflictDiff: "",
+            message: stdout.trim() || `Merged ${branchName}`,
+        };
+    }
+    catch (err) {
+        const errMsg = String(err);
+        // Check for merge conflicts
+        if (errMsg.includes("CONFLICT") || errMsg.includes("Merge conflict")) {
+            try {
+                // Get list of conflicted files
+                const { stdout: conflicted } = await git(["diff", "--name-only", "--diff-filter=U"], repoRoot);
+                const conflicts = conflicted.trim().split("\n").filter(Boolean);
+                // Capture the conflict diff (shows <<<<<<< markers)
+                let conflictDiff = "";
+                try {
+                    const { stdout: diff } = await git(["diff"], repoRoot);
+                    conflictDiff = diff.slice(0, 5000); // Cap at 5KB
+                }
+                catch {
+                    // diff might fail in weird states
+                }
+                // Abort the merge to restore clean state
+                await abortMergeSafe(repoRoot);
+                return {
+                    success: false,
+                    branch: branchName,
+                    conflicts,
+                    conflictDiff,
+                    message: `Merge conflicts in: ${conflicts.join(", ")}`,
+                };
+            }
+            catch {
+                await abortMergeSafe(repoRoot);
+                return {
+                    success: false,
+                    branch: branchName,
+                    conflicts: [],
+                    conflictDiff: "",
+                    message: errMsg,
+                };
+            }
+        }
+        return {
+            success: false,
+            branch: branchName,
+            conflicts: [],
+            conflictDiff: "",
+            message: errMsg,
+        };
+    }
+}
+/**
+ * Merge all completed thread branches sequentially.
+ *
+ * Supports:
+ *   - Custom merge order via options.order
+ *   - Partial merge: by default continues past conflicts (skips conflicting branch)
+ */
+export async function mergeAllThreads(repoRoot, threads, options = {}) {
+    const canonicalRepoRoot = assertWithinRepository(repoRoot, repoRoot);
+    const { order, continueOnConflict = true, userOverride, isFromRepoConfig, isAutoMerge } = options;
+    const results = [];
+    // Filter strictly to threads passing isEligibleForMerge with a valid branch
+    const eligible = threads.filter((t) => Boolean(t.branchName) &&
+        isEligibleForMerge(t, {
+            isAutoMerge,
+            userOverride,
+            isFromRepoConfig,
+        }).eligible);
+    // Apply ordering if specified
+    let ordered;
+    if (order && order.length > 0) {
+        const orderMap = new Map(order.map((id, idx) => [id, idx]));
+        ordered = [...eligible].sort((a, b) => {
+            const aIdx = orderMap.get(a.id) ?? Infinity;
+            const bIdx = orderMap.get(b.id) ?? Infinity;
+            return aIdx - bIdx;
+        });
+    }
+    else {
+        // Default: merge in completion order (earliest first)
+        ordered = [...eligible].sort((a, b) => (a.completedAt || 0) - (b.completedAt || 0));
+    }
+    for (const thread of ordered) {
+        const result = await mergeThreadBranch(canonicalRepoRoot, thread.branchName, thread.id, thread);
+        results.push(result);
+        if (!result.success && !continueOnConflict) {
+            // Stop on first conflict (legacy behavior)
+            break;
+        }
+        // If conflict but continueOnConflict is true, we skip this branch
+        // and proceed to the next. The merge was already aborted in mergeThreadBranch.
+    }
+    return results;
+}
+//# sourceMappingURL=merge.js.map

package/dist/worktree/merge.js.map

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package/package.json

@@ -0,0 +1,63 @@
+{
+  "name": "contextos-mcp",
+  "version": "0.4.0",
+  "description": "ContextOS Execution Layer and MCP Server",
+  "type": "module",
+  "bin": {
+    "contextos-mcp": "./bin/mcp.mjs"
+  },
+  "files": [
+    "dist",
+    "bin"
+  ],
+  "scripts": {
+    "dev": "tsx src/main.ts",
+    "build": "node scripts/clean-dist.cjs && tsc && npm run build:bundle && node -e \"require('fs').mkdirSync('dist/core', {recursive: true}); require('fs').copyFileSync('src/core/runtime.py', 'dist/core/runtime.py'); require('fs').cpSync('src/runtime', 'dist/runtime', {recursive: true});\"",
+    "build:bundle": "esbuild src/mcp/server.ts --bundle --platform=node --target=node20 --format=esm --outfile=dist/mcp/server.js --banner:js=\"import { createRequire as topLevelCreateRequire } from 'module'; const require = topLevelCreateRequire(import.meta.url);\" && esbuild src/plugins/adapter.ts --bundle --platform=node --target=node20 --format=cjs --outfile=../.agents/runtime/plugin-supply-chain-bundle.js",
+    "build:supply-chain": "esbuild src/plugins/adapter.ts --bundle --platform=node --target=node20 --format=cjs --outfile=../.agents/runtime/plugin-supply-chain-bundle.js",
+    "start": "node dist/main.js",
+    "cli": "tsx src/labs/cli.ts",
+    "swarm": "tsx src/main.ts",
+    "bench:oolong": "tsx benchmarks/oolong_synth.ts",
+    "bench:longbench": "tsx benchmarks/longbench_narrativeqa.ts",
+    "test": "vitest run",
+    "test:watch": "vitest",
+    "lint": "biome check src/ tests/",
+    "lint:fix": "biome check --fix src/ tests/",
+    "prepublishOnly": "npm run build"
+  },
+  "keywords": [
+    "mcp",
+    "model-context-protocol",
+    "contextos",
+    "coding-agent",
+    "execution-runtime",
+    "ai",
+    "subagents",
+    "worktree"
+  ],
+  "license": "MIT",
+  "homepage": "https://github.com/kok-o/contextos-agents#readme",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/kok-o/contextos-agents.git"
+  },
+  "dependencies": {
+    "@mariozechner/pi-ai": "^0.55.1",
+    "@modelcontextprotocol/sdk": "^1.27.1",
+    "typescript": "^5.7.0",
+    "zod": "^4.3.6"
+  },
+  "devDependencies": {
+    "@biomejs/biome": "^2.4.7",
+    "esbuild": "^0.27.3",
+    "tsx": "^4.19.0",
+    "vitest": "^4.1.0"
+  },
+  "engines": {
+    "node": ">=20"
+  },
+  "overrides": {
+    "minimatch": ">=10.2.1"
+  }
+}