@claudexor/workspace 1.0.1 → 2.1.3

package/dist/manager.js

@@ -4,9 +4,8 @@ import { tmpdir } from "node:os";
 import { join, sep } from "node:path";
 import { WorkspaceEnvelope as WorkspaceEnvelopeSchema } from "@claudexor/schema";
 import { runCaptureRaw, WorkspaceError } from "@claudexor/core";
-import { ensureDir, newId, nowIso } from "@claudexor/util";
+import { ensureDir, newId, nowIso, projectRuntimeDir } from "@claudexor/util";
 import { branchDelete, diffStaged, diffTrees, isGitRepo, revParse, snapshotTree, statusPorcelain, stashCreate, worktreeAdd, worktreePrune, worktreeRemove, } from "./git.js";
-import { ensureSelfIgnore } from "./self-ignore.js";
 /**
  * Manages WorkspaceEnvelopes: an isolated git worktree plus scoped HOME and
  * per-harness config dirs, and dirty-tree handling. Claudexor owns these
@@ -17,7 +16,9 @@ import { ensureSelfIgnore } from "./self-ignore.js";
  * (command names/titles mutate; the kernel start time never does). */
 export function processStartTime(pid) {
     try {
-        const out = execFileSync("ps", ["-p", String(pid), "-o", "lstart="], { encoding: "utf8" }).trim();
+        const out = execFileSync("ps", ["-p", String(pid), "-o", "lstart="], {
+            encoding: "utf8",
+        }).trim();
         return out.length > 0 ? out : null;
     }
     catch {
@@ -26,11 +27,13 @@ export function processStartTime(pid) {
 }
 export class WorkspaceManager {
     repoRoot;
-    constructor(repoRoot) {
+    runtimeRoot;
+    constructor(repoRoot, options = {}) {
         this.repoRoot = repoRoot;
+        this.runtimeRoot = options.runtimeRoot ?? projectRuntimeDir(repoRoot);
     }
     workspacesDir() {
-        return join(this.repoRoot, ".claudexor", "workspaces");
+        return join(this.runtimeRoot, "workspaces");
     }
     /**
      * The scoped envelope base for a task/attempt. The sole on-disk root we
@@ -40,7 +43,10 @@ export class WorkspaceManager {
      */
     envelopeBase(taskId, attemptId) {
         const idPattern = /^[A-Za-z0-9._-]+$/;
-        for (const [label, id] of [["taskId", taskId], ["attemptId", attemptId]]) {
+        for (const [label, id] of [
+            ["taskId", taskId],
+            ["attemptId", attemptId],
+        ]) {
             if (!idPattern.test(id) || id === "." || id === "..") {
                 throw new WorkspaceError(`${label} '${id}' is not a safe path segment`);
             }
@@ -53,17 +59,13 @@ export class WorkspaceManager {
     }
     async create(opts) {
         // Envelope base holds scoped dirs (HOME + per-harness config) and, for git
-        // mode, the worktree as a subdir — so harness-written HOME state (auth tokens,
-        // caches, plugins, session logs) lives outside the work tree and never lands
-        // in a diff.
+        // mode, the worktree as a subdir — so harness-written caches, plugins,
+        // transcripts, and route-scoped API auth state live outside the work tree
+        // and never land in a diff. Credentials are never copied into this
+        // envelope; adapters may add only capability-declared, vendor-specific
+        // child context (Claude/Cursor macOS Keychain bridge, INV-067).
         const base = this.envelopeBase(opts.taskId, opts.attemptId);
         ensureDir(base);
-        // Self-ignoring runtime dir: a `.gitignore` with `*` INSIDE .claudexor makes
-        // the whole dir invisible to git in PRE-EXISTING repos too (v0.9 widened the
-        // seeded credentials from API keys to subscription OAuth copies; a user's
-        // `git add -A` in their own repo must never capture them). Content-checked
-        // repair lives in the shared ensureSelfIgnore owner.
-        ensureSelfIgnore(join(this.repoRoot, ".claudexor"));
         const homeDir = join(base, "home");
         const codexHome = join(homeDir, ".codex");
         const claudeConfig = join(homeDir, ".claude");
@@ -84,7 +86,11 @@ export class WorkspaceManager {
         // daemon-tracked runs. Pid + ps START TIME form a recycling-proof identity
         // (command names/titles mutate — vitest, daemons and tools retitle
         // themselves; the kernel start time never does).
-        writeFileSync(join(base, "owner.json"), JSON.stringify({ pid: process.pid, started: processStartTime(process.pid), created_at: nowIso() }) + "\n");
+        writeFileSync(join(base, "owner.json"), JSON.stringify({
+            pid: process.pid,
+            started: processStartTime(process.pid),
+            created_at: nowIso(),
+        }) + "\n");
         // In-place mode: mutate the live repoRoot directly (no isolated worktree).
         // Used for thread turns (chat-first: the next turn sees this one's work) and
         // for stateful external environments where runtime state is the deliverable.
@@ -153,15 +159,14 @@ export class WorkspaceManager {
     }
     /**
      * Best-effort baseline copy of the live tree for in-place diff(). Copies each
-     * top-level entry individually (skipping heavy/ephemeral dirs, notably `.claudexor`
-     * which holds this base) — this both prunes noise and avoids Node's "cannot copy
-     * a directory into its own subdirectory" guard, since the baseline lives under
-     * `.claudexor`. On any failure the baseline is simply absent and diff() returns
-     * empty; reviewers still read the live tree directly.
+     * top-level entry individually while skipping only VCS/heavy ephemeral dirs.
+     * The baseline is external, so project `.claudexor/` content is ordinary user
+     * state and is copied like every other project path. On any failure the
+     * baseline is absent and diff() returns empty; reviewers still read the tree.
      */
     snapshotBaseline(base) {
         const baseline = join(base, "baseline");
-        const skip = new Set([".git", ".claudexor", "node_modules", "__pycache__", ".venv", "venv"]);
+        const skip = new Set([".git", "node_modules", "__pycache__", ".venv", "venv"]);
         try {
             ensureDir(baseline);
             for (const entry of readdirSync(this.repoRoot)) {
@@ -192,10 +197,12 @@ export class WorkspaceManager {
      * but a harness still writes native state — claude-code plan files, codex
      * session rollouts, transcripts — into `$HOME/.claude`, `$CODEX_HOME`, etc.
      * Without this, those land in the operator's REAL home (a live-caught leak: a
-     * read-only `plan` wrote into `~/.claude/plans`). Same env shape as `envFor`,
-     * so the adapters seed auth (subscription creds / api key) into these scoped
-     * dirs exactly as they do for a write envelope (CLAUDEXOR_BIBLE §6). Caller
-     * disposes when the run ends.
+     * read-only `plan` wrote into `~/.claude/plans`). Same env shape as `envFor`:
+     * non-native state and injected API-key routes stay scoped. This GENERIC
+     * home never bridges the OS Keychain; an adapter that declares
+     * `scoped_home_keychain_bridge` may create a vendor-only disposable child
+     * HOME without copying credentials (INV-067). Caller disposes all scoped
+     * state when the run ends.
      */
     readOnlyHomeEnv() {
         // A throwaway temp base — never under the project / synthetic repo root, so a
@@ -209,7 +216,12 @@ export class WorkspaceManager {
         for (const d of [homeDir, codexHome, claudeConfig, cursorConfig, opencodeConfig])
             ensureDir(d);
         return {
-            env: { HOME: homeDir, CODEX_HOME: codexHome, CLAUDE_CONFIG_DIR: claudeConfig, XDG_CONFIG_HOME: join(homeDir, ".config") },
+            env: {
+                HOME: homeDir,
+                CODEX_HOME: codexHome,
+                CLAUDE_CONFIG_DIR: claudeConfig,
+                XDG_CONFIG_HOME: join(homeDir, ".config"),
+            },
             dispose: () => {
                 try {
                     rmSync(base, { recursive: true, force: true });
@@ -294,14 +306,30 @@ export class WorkspaceManager {
             if (!existsSync(baseline))
                 return "";
             try {
-                const r = await runCaptureRaw("diff", ["-ruN", "-x", ".git", "-x", ".claudexor", "-x", ".claudexor-review-evidence", "-x", "node_modules", "-x", "__pycache__", "-x", ".venv", "-x", "venv", baseline, env.repo_root], { timeoutMs: 120_000 });
+                const r = await runCaptureRaw("diff", [
+                    "-ruN",
+                    "-x",
+                    ".git",
+                    "-x",
+                    "node_modules",
+                    "-x",
+                    "__pycache__",
+                    "-x",
+                    ".venv",
+                    "-x",
+                    "venv",
+                    baseline,
+                    env.repo_root,
+                ], { timeoutMs: 120_000 });
                 // Relativize the header paths to the git-style a/<rel> b/<rel> shape.
                 // Downstream consumers (diffstat, protected-path/risk gating) match
                 // REPO-RELATIVE globs like `test/**`; absolute `/…/repo/test/x`
                 // headers would silently bypass every one of them.
                 const relativized = WorkspaceManager.relativizePlainDiffHeadersFor(r.stdout, baseline, env.repo_root);
                 const CAP = 200_000;
-                return relativized.length > CAP ? relativized.slice(0, CAP) + "\n... [diff truncated]\n" : relativized;
+                return relativized.length > CAP
+                    ? relativized.slice(0, CAP) + "\n... [diff truncated]\n"
+                    : relativized;
             }
             catch {
                 // best-effort: if `diff` is unavailable the loop still works (reviewers read the live tree)
@@ -334,9 +362,9 @@ export class WorkspaceManager {
             }
         }
         // Remove only the scoped envelope base (worktree + scoped home/env/logs/artifacts/
-        // baseline, including any seeded credentials), derived from task/attempt ids.
+        // baseline, including any route-scoped API auth material), derived from task/attempt ids.
         // For git mode this equals dirname(worktree_path); for in-place it is a sibling
-        // under `.claudexor/workspaces`, so deriving from ids is exactly what prevents
+        // under the external runtime workspaces root, so deriving from ids prevents
         // dispose() from ever deleting the live tree.
         try {
             rmSync(this.envelopeBase(env.task_id, env.attempt_id), { recursive: true, force: true });

package/dist/manager.js.map

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package/dist/raw-patch.d.ts

@@ -0,0 +1,17 @@
+import type { HarnessEvent, RawContextPacket, RawGitPatchEnvelope, RawPatchRefusalCode } from "@claudexor/schema";
+export declare class RawPatchRefusalError extends Error {
+    readonly code: RawPatchRefusalCode;
+    constructor(code: RawPatchRefusalCode, message: string);
+}
+export declare function captureRawPatchEnvelope(enabled: boolean, previous: RawGitPatchEnvelope | null, event: HarnessEvent): RawGitPatchEnvelope | null;
+/** Validate and materialize a raw patch only inside its isolated candidate tree. */
+export declare function consumeRawPatchEnvelope(input: {
+    repoRoot: string;
+    worktreePath: string;
+    baseCommitSha: string;
+    context: RawContextPacket | null;
+    envelope: RawGitPatchEnvelope | null;
+}): Promise<{
+    materializedTreeSha: string;
+}>;
+//# sourceMappingURL=raw-patch.d.ts.map

package/dist/raw-patch.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"raw-patch.d.ts","sourceRoot":"","sources":["../src/raw-patch.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EACV,YAAY,EACZ,gBAAgB,EAChB,mBAAmB,EACnB,mBAAmB,EACpB,MAAM,mBAAmB,CAAC;AAI3B,qBAAa,oBAAqB,SAAQ,KAAK;aAE3B,IAAI,EAAE,mBAAmB;gBAAzB,IAAI,EAAE,mBAAmB,EACzC,OAAO,EAAE,MAAM;CAKlB;AAuBD,wBAAgB,uBAAuB,CACrC,OAAO,EAAE,OAAO,EAChB,QAAQ,EAAE,mBAAmB,GAAG,IAAI,EACpC,KAAK,EAAE,YAAY,GAClB,mBAAmB,GAAG,IAAI,CAQ5B;AAED,oFAAoF;AACpF,wBAAsB,uBAAuB,CAAC,KAAK,EAAE;IACnD,QAAQ,EAAE,MAAM,CAAC;IACjB,YAAY,EAAE,MAAM,CAAC;IACrB,aAAa,EAAE,MAAM,CAAC;IACtB,OAAO,EAAE,gBAAgB,GAAG,IAAI,CAAC;IACjC,QAAQ,EAAE,mBAAmB,GAAG,IAAI,CAAC;CACtC,GAAG,OAAO,CAAC;IAAE,mBAAmB,EAAE,MAAM,CAAA;CAAE,CAAC,CA0H3C"}

package/dist/raw-patch.js

@@ -0,0 +1,158 @@
+import { isAbsolute, resolve } from "node:path";
+import { parseUnifiedDiff } from "@claudexor/core";
+import { sensitiveResourcePolicy, sha256 } from "@claudexor/util";
+import { applyPatchProtected, git, materializePatchTree, revParse } from "./git.js";
+export class RawPatchRefusalError extends Error {
+    code;
+    constructor(code, message) {
+        super(message);
+        this.code = code;
+        this.name = "RawPatchRefusalError";
+    }
+}
+function refuse(code, detail) {
+    throw new RawPatchRefusalError(code, `${code}: ${detail}`);
+}
+function validatePath(path) {
+    if (!path ||
+        isAbsolute(path) ||
+        path.includes("\\") ||
+        path.split("/").some((part) => part === ".." || part === "" || part === ".")) {
+        refuse("raw_patch_path_traversal", `invalid repo-relative path ${JSON.stringify(path)}`);
+    }
+}
+function rootAllows(path, root) {
+    if (root === ".")
+        return true;
+    validatePath(root);
+    return path === root || path.startsWith(`${root}/`);
+}
+export function captureRawPatchEnvelope(enabled, previous, event) {
+    if (event.type !== "patch_produced")
+        return previous;
+    if (!enabled || !event.patch_envelope || previous)
+        refuse("raw_patch_missing_evidence", "expected exactly one enabled patch envelope");
+    if (sensitiveResourcePolicy.containsSensitiveContent(event.patch_envelope.patch)) {
+        refuse("raw_patch_sensitive_content", "patch content matched sensitive-resource policy");
+    }
+    return event.patch_envelope;
+}
+/** Validate and materialize a raw patch only inside its isolated candidate tree. */
+export async function consumeRawPatchEnvelope(input) {
+    const { repoRoot, worktreePath, baseCommitSha, context, envelope } = input;
+    if (!context || !envelope)
+        refuse("raw_patch_missing_evidence", "raw producer returned no patch envelope");
+    if (resolve(repoRoot) === resolve(worktreePath)) {
+        refuse("raw_patch_requires_isolation", "raw patches cannot materialize in the live tree");
+    }
+    if (envelope.context_packet_hash !== context.packet_hash) {
+        refuse("raw_patch_missing_evidence", "response does not bind the supplied context packet");
+    }
+    const actualBaseTree = await revParse(repoRoot, `${baseCommitSha}^{tree}`);
+    if (context.base_commit_sha !== baseCommitSha ||
+        context.base_tree_sha !== actualBaseTree ||
+        envelope.base_tree_sha !== actualBaseTree) {
+        refuse("raw_patch_base_mismatch", "patch and context do not bind the candidate base tree");
+    }
+    let worktreeBaseTree;
+    try {
+        worktreeBaseTree = await revParse(worktreePath, "HEAD^{tree}");
+    }
+    catch {
+        refuse("raw_patch_requires_isolation", "isolated worktree base could not be verified");
+    }
+    if (worktreeBaseTree !== actualBaseTree) {
+        refuse("raw_patch_base_mismatch", "isolated worktree HEAD does not match the bound base tree");
+    }
+    const worktreeStatus = await git(worktreePath, [
+        "status",
+        "--porcelain=v1",
+        "-z",
+        "--untracked-files=all",
+    ]);
+    if (worktreeStatus.code !== 0) {
+        refuse("raw_patch_requires_isolation", "isolated worktree status could not be verified");
+    }
+    if (worktreeStatus.stdout.length !== 0) {
+        refuse("raw_patch_requires_isolation", "isolated worktree must be clean before raw apply");
+    }
+    if (sha256(envelope.patch) !== envelope.patch_hash) {
+        refuse("raw_patch_digest_mismatch", "patch_hash does not match the exact patch bytes");
+    }
+    const parsed = parseUnifiedDiff(envelope.patch);
+    if (parsed.files.length === 0)
+        refuse("raw_patch_truncated", "patch has no complete file record");
+    if (parsed.files.some((file) => file.binary)) {
+        refuse("raw_patch_binary_unsupported", "binary patch payloads are not accepted by raw API");
+    }
+    const actualPaths = new Set();
+    const expectedPresence = new Map();
+    for (const file of parsed.files) {
+        if (file.oldPath) {
+            validatePath(file.oldPath);
+            actualPaths.add(file.oldPath);
+            expectedPresence.set(file.oldPath, "present");
+        }
+        if (file.newPath) {
+            validatePath(file.newPath);
+            actualPaths.add(file.newPath);
+            const expected = file.oldPath === file.newPath ? "present" : "absent";
+            const prior = expectedPresence.get(file.newPath);
+            if (prior && prior !== expected) {
+                refuse("raw_patch_missing_evidence", `conflicting base-tree operations for ${file.newPath}`);
+            }
+            expectedPresence.set(file.newPath, expected);
+        }
+    }
+    const editable = new Map(context.readable_files.map((file) => [file.path, file]));
+    const declared = new Map();
+    for (const item of envelope.touched_paths) {
+        validatePath(item.path);
+        if (declared.has(item.path)) {
+            refuse("raw_patch_missing_evidence", `duplicate evidence for ${item.path}`);
+        }
+        declared.set(item.path, item.expected_blob_oid);
+    }
+    for (const path of actualPaths) {
+        if (sensitiveResourcePolicy.classifyPath(path).sensitive) {
+            refuse("raw_patch_outside_scope", `${path} is outside the packet's exact editable scope`);
+        }
+        const presence = expectedPresence.get(path);
+        const file = editable.get(path);
+        const expected = declared.get(path);
+        if (expected === undefined || !presence) {
+            refuse("raw_patch_missing_evidence", `missing preimage evidence for ${path}`);
+        }
+        if (presence === "present") {
+            if (!context.editable_paths.includes(path) || !file) {
+                refuse("raw_patch_outside_scope", `${path} is outside the packet's exact editable scope`);
+            }
+            if (file.blob_oid !== expected) {
+                refuse("raw_patch_stale_preimage", `preimage oid for ${path} does not match the packet`);
+            }
+            continue;
+        }
+        if (!context.creatable_roots.some((root) => rootAllows(path, root))) {
+            refuse("raw_patch_outside_scope", `${path} is outside the packet's exact create scope`);
+        }
+        if (file || expected !== null) {
+            refuse("raw_patch_stale_preimage", `preimage oid for ${path} does not match the packet`);
+        }
+    }
+    if (declared.size !== actualPaths.size ||
+        [...declared].some(([path]) => !actualPaths.has(path))) {
+        refuse("raw_patch_missing_evidence", "declared touched paths differ from the Git patch");
+    }
+    let materializedTreeSha;
+    try {
+        materializedTreeSha = await materializePatchTree(repoRoot, baseCommitSha, envelope.patch);
+    }
+    catch (error) {
+        refuse("raw_patch_apply_failed", error instanceof Error ? error.message : String(error));
+    }
+    const applied = await applyPatchProtected(worktreePath, envelope.patch);
+    if (!applied.ok)
+        refuse("raw_patch_apply_failed", applied.detail ?? "git apply refused");
+    return { materializedTreeSha };
+}
+//# sourceMappingURL=raw-patch.js.map

package/dist/raw-patch.js.map

@@ -0,0 +1 @@
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package/dist/thread-tree.d.ts

@@ -13,8 +13,15 @@ export interface ThreadWorktreeResult {
  * the cumulative patch to the project. Race candidates still branch off the
  * worktree's current state into throwaway envelopes.
  *
- * The worktree lives under the project's self-ignored `.claudexor/`, so the
- * project's own git never sees it and snapshots exclude it.
+ * The worktree lives in Claudexor's external per-project runtime namespace;
+ * the project's own git and ignore files are never used as a runtime boundary.
  */
 export declare function ensureThreadWorktree(projectRoot: string, threadId: string): Promise<ThreadWorktreeResult>;
+/** Advance the persistent thread branch to the project state just delivered,
+ * then realign its daemon-owned worktree. The branch ref makes snapshot
+ * commits survive aggressive Git GC; the returned SHA is the journal base. */
+export declare function advanceThreadWorktree(projectRoot: string, threadId: string, worktreePath: string, targetSha: string): Promise<string>;
+/** Explicit purge of daemon-owned isolated-thread resources. Lifecycle
+ * authority lives in the journal; the generic orphan sweeper never guesses. */
+export declare function purgeThreadWorktree(projectRoot: string, threadId: string): Promise<void>;
 //# sourceMappingURL=thread-tree.d.ts.map

package/dist/thread-tree.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"thread-tree.d.ts","sourceRoot":"","sources":["../src/thread-tree.ts"],"names":[],"mappings":"AAOA,MAAM,WAAW,oBAAoB;IACnC,8EAA8E;IAC9E,IAAI,EAAE,MAAM,CAAC;IACb,oEAAoE;IACpE,OAAO,EAAE,MAAM,CAAC;IAChB,2DAA2D;IAC3D,OAAO,EAAE,OAAO,CAAC;CAClB;AAED;;;;;;;;;GASG;AACH,wBAAsB,oBAAoB,CAAC,WAAW,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,oBAAoB,CAAC,CAiD/G"}
+{"version":3,"file":"thread-tree.d.ts","sourceRoot":"","sources":["../src/thread-tree.ts"],"names":[],"mappings":"AAeA,MAAM,WAAW,oBAAoB;IACnC,8EAA8E;IAC9E,IAAI,EAAE,MAAM,CAAC;IACb,oEAAoE;IACpE,OAAO,EAAE,MAAM,CAAC;IAChB,2DAA2D;IAC3D,OAAO,EAAE,OAAO,CAAC;CAClB;AAED;;;;;;;;;GASG;AACH,wBAAsB,oBAAoB,CACxC,WAAW,EAAE,MAAM,EACnB,QAAQ,EAAE,MAAM,GACf,OAAO,CAAC,oBAAoB,CAAC,CA6C/B;AAED;;8EAE8E;AAC9E,wBAAsB,qBAAqB,CACzC,WAAW,EAAE,MAAM,EACnB,QAAQ,EAAE,MAAM,EAChB,YAAY,EAAE,MAAM,EACpB,SAAS,EAAE,MAAM,GAChB,OAAO,CAAC,MAAM,CAAC,CA0BjB;AAED;+EAC+E;AAC/E,wBAAsB,mBAAmB,CAAC,WAAW,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAS9F"}

package/dist/thread-tree.js

@@ -1,9 +1,8 @@
 import { existsSync, rmSync } from "node:fs";
 import { join } from "node:path";
 import { WorkspaceError } from "@claudexor/core";
-import { ensureDir } from "@claudexor/util";
-import { branchDelete, isGitRepo, revParse, snapshotTree, worktreeAdd, worktreeAddExisting } from "./git.js";
-import { ensureSelfIgnore } from "./self-ignore.js";
+import { ensureDir, projectRuntimeDir } from "@claudexor/util";
+import { branchDelete, git, isGitRepo, revParse, snapshotTree, worktreeAdd, worktreeAddExisting, worktreeRemove, } from "./git.js";
 /**
  * Lazily create (or reuse) the persistent git worktree backing an ISOLATED
  * thread. Turns run in-place WITHIN this worktree so each sees the previous
@@ -11,8 +10,8 @@ import { ensureSelfIgnore } from "./self-ignore.js";
  * the cumulative patch to the project. Race candidates still branch off the
  * worktree's current state into throwaway envelopes.
  *
- * The worktree lives under the project's self-ignored `.claudexor/`, so the
- * project's own git never sees it and snapshots exclude it.
+ * The worktree lives in Claudexor's external per-project runtime namespace;
+ * the project's own git and ignore files are never used as a runtime boundary.
  */
 export async function ensureThreadWorktree(projectRoot, threadId) {
     if (!/^[A-Za-z0-9._-]+$/.test(threadId) || threadId === "." || threadId === "..") {
@@ -21,19 +20,15 @@ export async function ensureThreadWorktree(projectRoot, threadId) {
     if (!(await isGitRepo(projectRoot))) {
         throw new WorkspaceError(`isolated threads require a git project: ${projectRoot}`);
     }
-    const path = join(projectRoot, ".claudexor", "threads", threadId, "tree");
+    const threadDir = join(projectRuntimeDir(projectRoot), "threads", threadId);
+    const path = join(threadDir, "tree");
     if (existsSync(join(path, ".git"))) {
         // Turns never commit on the branch (in-place envelopes leave changes in the
         // working tree), so HEAD still points at the original base snapshot.
         return { path, baseSha: await revParse(path, "HEAD"), created: false };
     }
     const baseSha = await snapshotTree(projectRoot);
-    const threadDir = join(projectRoot, ".claudexor", "threads", threadId);
     ensureDir(threadDir);
-    // Self-ignore the project's `.claudexor/` so the user's own `git add -A` never
-    // captures the thread worktree (shared content-checked owner with
-    // WorkspaceManager: a user-edited/emptied file is repaired, not trusted).
-    ensureSelfIgnore(join(projectRoot, ".claudexor"));
     const branch = `claudexor/thread-${threadId}`;
     // Thread branches are PERSISTENT live-thread state. When the branch
     // survives but the worktree directory was lost, RECOVER by recreating the
@@ -66,4 +61,47 @@ export async function ensureThreadWorktree(projectRoot, threadId) {
     }
     return { path, baseSha, created: true };
 }
+/** Advance the persistent thread branch to the project state just delivered,
+ * then realign its daemon-owned worktree. The branch ref makes snapshot
+ * commits survive aggressive Git GC; the returned SHA is the journal base. */
+export async function advanceThreadWorktree(projectRoot, threadId, worktreePath, targetSha) {
+    if (!/^[A-Za-z0-9._-]+$/.test(threadId) || threadId === "." || threadId === "..") {
+        throw new WorkspaceError(`threadId '${threadId}' is not a safe path segment`);
+    }
+    const branch = `refs/heads/claudexor/thread-${threadId}`;
+    const oldTip = await revParse(projectRoot, branch);
+    // Materialize the target in the daemon-owned index/worktree without moving
+    // HEAD. Publishing the persistent branch first would make a failed reset or
+    // clean look authoritative even though the worktree still held older work.
+    const realign = await git(worktreePath, ["read-tree", "--reset", "-u", targetSha]);
+    if (realign.code !== 0) {
+        throw new WorkspaceError(`thread worktree realignment failed: ${realign.stderr.trim()}`);
+    }
+    const clean = await git(worktreePath, ["clean", "-fd"]);
+    if (clean.code !== 0) {
+        throw new WorkspaceError(`thread worktree cleanup failed: ${clean.stderr.trim()}`);
+    }
+    const update = await git(projectRoot, ["update-ref", branch, targetSha, oldTip]);
+    if (update.code !== 0) {
+        throw new WorkspaceError(`thread branch advanced concurrently: ${update.stderr.trim()}`);
+    }
+    const observed = await revParse(worktreePath, "HEAD");
+    if (observed !== targetSha) {
+        throw new WorkspaceError("thread branch and worktree did not converge on the delivered SHA");
+    }
+    return targetSha;
+}
+/** Explicit purge of daemon-owned isolated-thread resources. Lifecycle
+ * authority lives in the journal; the generic orphan sweeper never guesses. */
+export async function purgeThreadWorktree(projectRoot, threadId) {
+    if (!/^[A-Za-z0-9._-]+$/.test(threadId) || threadId === "." || threadId === "..") {
+        throw new WorkspaceError(`threadId '${threadId}' is not a safe path segment`);
+    }
+    const threadDir = join(projectRuntimeDir(projectRoot), "threads", threadId);
+    const path = join(threadDir, "tree");
+    if (existsSync(join(path, ".git")))
+        await worktreeRemove(projectRoot, path);
+    rmSync(threadDir, { recursive: true, force: true });
+    await branchDelete(projectRoot, `claudexor/thread-${threadId}`).catch(() => { });
+}
 //# sourceMappingURL=thread-tree.js.map

package/dist/thread-tree.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@claudexor/workspace",
-  "version": "1.0.1",
+  "version": "2.1.3",
   "license": "MIT",
   "description": "WorkspaceEnvelope manager: git worktree + scoped HOME/harness-config isolation + dirty policy.",
   "type": "module",
@@ -16,9 +16,9 @@
     "dist"
   ],
   "dependencies": {
-    "@claudexor/schema": "1.0.1",
-    "@claudexor/util": "1.0.1",
-    "@claudexor/core": "1.0.1"
+    "@claudexor/core": "2.1.3",
+    "@claudexor/schema": "2.1.3",
+    "@claudexor/util": "2.1.3"
   },
   "repository": {
     "type": "git",

package/dist/self-ignore.d.ts

@@ -1,10 +0,0 @@
-/**
- * Ensure `.claudexor/.gitignore` CONTAINS `*` so the runtime dir stays
- * invisible to the project's git (the git-native trick that avoids mutating
- * the user's own .gitignore). Content-checked, not just existence-checked:
- * a user-edited or emptied file would silently re-expose envelopes, thread
- * worktrees, and seeded credentials to `git add -A`. Shared by the envelope
- * manager and the thread-worktree creator (single owner of the invariant).
- */
-export declare function ensureSelfIgnore(claudexorDir: string): void;
-//# sourceMappingURL=self-ignore.d.ts.map

package/dist/self-ignore.d.ts.map

@@ -1 +0,0 @@
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