@jentrix/cli 0.5.12 → 0.5.13

package/claude-plugin/.claude-plugin/plugin.json

@@ -1,5 +1,5 @@
 {
   "name": "jentrix",
   "description": "Connect this Claude Code session to a Jentrix project: /jentrix-connect binds the current session (trusted lifecycle hooks supply the session id), /jentrix-align runs the MVP alignment wizard, /jentrix-status and /jentrix-end wrap the same session operations. Business logic lives in the Jentrix CLI — removing this plugin leaves `jentrix session attach` as the universal fallback.",
-  "version": "0.5.0"
+  "version": "0.5.1"
 }

package/claude-plugin/commands/jentrix-align.md

@@ -59,7 +59,8 @@ and do NOT answer any question yourself.
     and move with
     `jentrix task move --task <taskId> --to-column-id <columnId>`. Use only
     the columns the board actually has — never invent a status. `/jentrix-end`
-    moves it to a terminal column when the work is genuinely finished. A
+    moves it to the In review column when the work is genuinely finished —
+    the terminal move is the operator's Accept, never yours. A
     board that never moves is a board that lies about what is in flight.
 11. If align wrote `./.mcp.json`, relay that line too: MCP servers load at
     session start, so the tools in THIS session still point wherever they

package/claude-plugin/hooks/hooks.json

@@ -1,12 +1,12 @@
 {
-  "description": "M20.1 \u00a715.1 \u2014 lifecycle bridge: hooks append their structured stdin payload (session_id, transcript_path, cwd) to the local session context file via `stacks-runner session-hook`. argv carries only the directory and event name \u2014 never credentials or transcript content. PreCompact/PostCompact additionally run `jentrix session snapshot`, which FOLLOWS THE CAPTURE CONSENT: capture ON preserves the transcript range about to leave the model's context; capture OFF (the MVP default) records the compaction boundary and NO content, because `capture: \"off\"` was disclosed as typed artifacts only, no transcript. Preservation is never distillation \u2014 a hook has no model turn; /jentrix-checkpoint does that. Compaction-path hooks carry an explicit 10s timeout (STA-51): they run inside the operator's /compact, and a slow artifact push must delay it by seconds, not the 60s default.",
+  "description": "M20.1 \u00a715.1 \u2014 lifecycle bridge: hooks append their structured stdin payload (session_id, transcript_path, cwd) to the local session context file via `stacks-runner session-hook`. argv carries only the provider and event name (the runner resolves the directory cross-platform \u2014 STA-131: a literal $HOME never expands in Windows hook commands) \u2014 never credentials or transcript content. PreCompact/PostCompact additionally run `jentrix session snapshot`, which FOLLOWS THE CAPTURE CONSENT: capture ON preserves the transcript range about to leave the model's context; capture OFF (the MVP default) records the compaction boundary and NO content, because `capture: \"off\"` was disclosed as typed artifacts only, no transcript. Preservation is never distillation \u2014 a hook has no model turn; /jentrix-checkpoint does that. Compaction-path hooks carry an explicit 10s timeout (STA-51): they run inside the operator's /compact, and a slow artifact push must delay it by seconds, not the 60s default.",
   "hooks": {
     "SessionStart": [
       {
         "hooks": [
           {
             "type": "command",
-            "command": "stacks-runner session-hook --dir \"$HOME/.config/stacks/claude-sessions\" --event SessionStart"
+            "command": "stacks-runner session-hook --provider claude --event SessionStart"
           }
         ]
       }
@@ -16,7 +16,7 @@
         "hooks": [
           {
             "type": "command",
-            "command": "stacks-runner session-hook --dir \"$HOME/.config/stacks/claude-sessions\" --event SessionEnd"
+            "command": "stacks-runner session-hook --provider claude --event SessionEnd"
           }
         ]
       }
@@ -26,7 +26,7 @@
         "hooks": [
           {
             "type": "command",
-            "command": "stacks-runner session-hook --dir \"$HOME/.config/stacks/claude-sessions\" --event PreCompact",
+            "command": "stacks-runner session-hook --provider claude --event PreCompact",
             "timeout": 10
           },
           {
@@ -42,7 +42,7 @@
         "hooks": [
           {
             "type": "command",
-            "command": "stacks-runner session-hook --dir \"$HOME/.config/stacks/claude-sessions\" --event PostCompact",
+            "command": "stacks-runner session-hook --provider claude --event PostCompact",
             "timeout": 10
           },
           {

package/codex-plugin/plugins/jentrix/.codex-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "jentrix",
-  "version": "0.2.0",
+  "version": "0.2.1",
   "description": "Connect Codex tasks to Jentrix projects with trusted lifecycle hooks, alignment, checkpoints, and honest session capture.",
   "author": {
     "name": "Jentrix",

package/codex-plugin/plugins/jentrix/hooks/hooks.json

@@ -6,7 +6,7 @@
         "hooks": [
           {
             "type": "command",
-            "command": "stacks-runner session-hook --dir \"$HOME/.config/stacks/codex-sessions\" --event SessionStart"
+            "command": "stacks-runner session-hook --provider codex --event SessionStart"
           }
         ]
       }
@@ -16,7 +16,7 @@
         "hooks": [
           {
             "type": "command",
-            "command": "stacks-runner session-hook --dir \"$HOME/.config/stacks/codex-sessions\" --event UserPromptSubmit"
+            "command": "stacks-runner session-hook --provider codex --event UserPromptSubmit"
           }
         ]
       }
@@ -26,7 +26,7 @@
         "hooks": [
           {
             "type": "command",
-            "command": "stacks-runner session-hook --dir \"$HOME/.config/stacks/codex-sessions\" --event PostToolUse"
+            "command": "stacks-runner session-hook --provider codex --event PostToolUse"
           }
         ]
       }
@@ -36,7 +36,7 @@
         "hooks": [
           {
             "type": "command",
-            "command": "stacks-runner session-hook --dir \"$HOME/.config/stacks/codex-sessions\" --event Stop"
+            "command": "stacks-runner session-hook --provider codex --event Stop"
           }
         ]
       }
@@ -46,7 +46,7 @@
         "hooks": [
           {
             "type": "command",
-            "command": "stacks-runner session-hook --dir \"$HOME/.config/stacks/codex-sessions\" --event PreCompact",
+            "command": "stacks-runner session-hook --provider codex --event PreCompact",
             "timeout": 10
           },
           {
@@ -62,7 +62,7 @@
         "hooks": [
           {
             "type": "command",
-            "command": "stacks-runner session-hook --dir \"$HOME/.config/stacks/codex-sessions\" --event PostCompact",
+            "command": "stacks-runner session-hook --provider codex --event PostCompact",
             "timeout": 10
           },
           {
@@ -78,7 +78,7 @@
         "hooks": [
           {
             "type": "command",
-            "command": "stacks-runner session-hook --dir \"$HOME/.config/stacks/codex-sessions\" --event SessionEnd"
+            "command": "stacks-runner session-hook --provider codex --event SessionEnd"
           }
         ]
       }

package/dist/main.js

@@ -20962,7 +20962,7 @@ function refreshAccessToken(input) {
 
 // src/client.ts
 var CLI_NAME = "stacks-cli";
-var CLI_VERSION = "0.5.12";
+var CLI_VERSION = "0.5.13";
 var DEAD_TOKEN_MESSAGE = "authentication failed (HTTP 401): the token is dead or expired \u2014 mint a new PAT at /account/tokens on your Jentrix server and update STACKS_TOKEN (or --token / the config file).";
 var RELOGIN_MESSAGE = "OAuth session expired and could not be refreshed \u2014 run `jentrix login` to sign in again.";
 function originOf2(url2) {
@@ -21909,6 +21909,30 @@ import {
   writeFileSync as writeFileSync2
 } from "node:fs";
 import { dirname as dirname2, join as join2 } from "node:path";
+
+// src/retry.ts
+async function withRateLimitRetry(fn, options) {
+  const { maxRetries, maxWaitSeconds, sleep, now } = options;
+  const start = now();
+  let attempt = 0;
+  for (; ; ) {
+    const result = await fn();
+    const envelope = envelopeOfResult(result);
+    if (envelope?.error.code !== "RATE_LIMITED") return result;
+    const retryAfter = envelope.error.retryAfterSeconds;
+    if (typeof retryAfter !== "number" || !Number.isFinite(retryAfter)) {
+      return result;
+    }
+    if (retryAfter < 0) return result;
+    if (attempt >= maxRetries) return result;
+    const elapsedMs = now() - start;
+    if (elapsedMs + retryAfter * 1e3 > maxWaitSeconds * 1e3) return result;
+    await sleep(retryAfter * 1e3);
+    attempt += 1;
+  }
+}
+
+// src/commands/session.ts
 var LEGACY_MARKER_KEY = "__v1__";
 function isMarker(value) {
   return typeof value === "object" && value !== null && typeof value.sessionId === "string";
@@ -22029,9 +22053,28 @@ function isRecord5(value) {
 async function callStructured(caller, name, args) {
   return call(caller, name, args);
 }
+var ToolCallError = class extends Error {
+  constructor(message, code = null) {
+    super(message);
+    this.code = code;
+  }
+  code;
+};
 async function call(caller, name, args) {
-  const result = await caller.callTool({ name, arguments: args });
+  const result = await withRateLimitRetry(
+    () => caller.callTool({ name, arguments: args }),
+    {
+      maxRetries: 2,
+      maxWaitSeconds: 60,
+      sleep: (ms) => new Promise((resolve5) => setTimeout(resolve5, ms)),
+      now: Date.now
+    }
+  );
   if (isRecord5(result) && result.isError === true) {
+    const envelope = envelopeOfResult(result);
+    if (envelope) {
+      throw new ToolCallError(envelope.error.message, envelope.error.code);
+    }
     let message = "tool call failed";
     if (Array.isArray(result.content)) {
       const text = result.content.find(
@@ -22046,7 +22089,7 @@ async function call(caller, name, args) {
         }
       }
     }
-    throw new Error(message);
+    throw new ToolCallError(message);
   }
   return isRecord5(result) && isRecord5(result.structuredContent) ? result.structuredContent : {};
 }
@@ -23573,6 +23616,26 @@ function registerSessionCommand(program3, deps2, onExit2) {
 }
 
 // src/commands/align.ts
+async function resolveWorkspaceFlag(caller, wanted, pinned) {
+  const listed = await callStructured(caller, "list_workspaces", {});
+  const rows = listed.workspaces ?? [];
+  const match = rows.find(
+    (ws) => ws.id === wanted || ws.slug === wanted.toLowerCase()
+  );
+  if (!match) {
+    throw new UsageError(
+      `--workspace ${wanted} matches none of your workspaces (slugs: ${rows.map((ws) => ws.slug).filter(Boolean).join(", ") || "none visible"})`,
+      EXIT_CODES.NOT_FOUND
+    );
+  }
+  if (pinned && pinned.id !== match.id) {
+    throw new UsageError(
+      `--workspace ${wanted} conflicts with this token's pinned workspace (${pinned.id})`,
+      EXIT_CODES.FORBIDDEN
+    );
+  }
+  return match.id;
+}
 var MAX_WORK_ITEMS = 15;
 async function projectBoards(caller, projectId) {
   const project = await callStructured(caller, "get_project", { projectId });
@@ -24364,10 +24427,17 @@ async function runAlign(flags, deps2) {
       let pendingCreateProject = null;
       if (flags.newTask) workItem = `__new__:${flags.newTask}`;
       if (flags.newProject && flags.newProject.trim()) {
-        const workspaceId = catalog.chosenWorkspaceId ?? catalog.pinnedWorkspace?.id ?? null;
+        let workspaceId = catalog.chosenWorkspaceId ?? catalog.pinnedWorkspace?.id ?? null;
+        if (flags.workspace?.trim()) {
+          workspaceId = await resolveWorkspaceFlag(
+            caller,
+            flags.workspace.trim(),
+            catalog.pinnedWorkspace ?? null
+          );
+        }
         if (!workspaceId) {
           throw new UsageError(
-            "--new-project needs a resolved workspace (a workspace-pinned token or a repo-matched candidate) \u2014 none resolved here"
+            "--new-project needs a resolved workspace (a workspace-pinned token, a repo-matched candidate, or --workspace <id-or-slug>) \u2014 none resolved here"
           );
         }
         pendingCreateProject = {
@@ -24694,6 +24764,9 @@ function registerAlignCommand(program3, deps2, onExit2) {
   ).option("--project <id-or-slug>", "project to align to").option(
     "--new-project <name>",
     "create a project in the resolved workspace (seeds a board + repo/board links), then align to it"
+  ).option(
+    "--workspace <id-or-slug>",
+    "workspace for --new-project when neither a pinned token nor a repo match resolves one (fresh checkout, non-interactive)"
   ).option("--task <taskId>", "existing work item to align to").option(
     "--new-task <title>",
     "create a task (existing ops core) and align to it"
@@ -24944,7 +25017,20 @@ async function basisBlock(refs, deps2) {
           });
           const record3 = result.artifact ?? result;
           titles.set(id, String(record3.title ?? ""));
-        } catch {
+        } catch (error2) {
+          const code = error2 instanceof ToolCallError ? error2.code : null;
+          if (code === "RATE_LIMITED") {
+            throw new UsageError(
+              `--basis ${id} could not be verified \u2014 the server is rate limiting reads; the ref may be fine. Retry the push shortly.`,
+              EXIT_CODES.RATE_LIMITED
+            );
+          }
+          if (code && code !== "NOT_FOUND" && code !== "FORBIDDEN") {
+            throw new UsageError(
+              `--basis ${id} could not be verified (${code}) \u2014 the ref may be fine. Retry the push.`,
+              EXIT_CODES.INTERNAL
+            );
+          }
           throw new UsageError(
             `--basis ${id} does not resolve to an artifact you can read \u2014 push the context first (\`jentrix push context\`), or pass a URL`,
             EXIT_CODES.NOT_FOUND
@@ -25023,7 +25109,7 @@ async function offerCardMint(kind, payload, flags, deps2, sessionId = null) {
       sessionId
     });
     deps2.writeOut(
-      `Minted ${minted.key ?? minted.id} on ${board.name} \xB7 artifact linked \xB7 ${flags.blocks ? "BLOCKS" : "RELATES_TO"} ${payload.taskId}`
+      `Minted ${minted.key ?? minted.id} on ${board.name} \xB7 ${minted.artifactLinked ? "artifact linked" : "artifact NOT linked (see note)"} \xB7 ${flags.blocks ? "BLOCKS" : "RELATES_TO"} ${payload.taskId}`
     );
   } catch (error2) {
     deps2.writeErr(
@@ -25068,7 +25154,7 @@ async function mintCard(deps2, input) {
         idempotencyKey: `mint-${input.artifactId}`
       });
       const issueId = String(created.id);
-      await (deps2.fetchImpl ?? fetch)(
+      const linkResponse = await (deps2.fetchImpl ?? fetch)(
         new URL(taskTarget(issueId).path, stacksBaseUrlOf(target.url)),
         {
           method: "POST",
@@ -25080,16 +25166,29 @@ async function mintCard(deps2, input) {
           body: JSON.stringify({ refArtifactId: input.artifactId })
         }
       );
+      const artifactLinked = linkResponse.ok;
+      if (!artifactLinked) {
+        deps2.writeErr(
+          `note: minted the card but linking artifact ${input.artifactId} to it failed (HTTP ${linkResponse.status}) \u2014 link it by hand: jentrix push ${pushKindForNoun(input.noun)} --task ${issueId} --ref ${input.artifactId}`
+        );
+      }
       await callStructured(caller, "add_task_link", {
         fromTaskId: issueId,
         toTaskId: input.anchorTaskId,
         kind: input.blocks ? "BLOCKS" : "RELATES_TO"
       });
-      return { id: issueId, key: created.key };
+      return {
+        id: issueId,
+        key: created.key,
+        artifactLinked
+      };
     },
     input.sessionId ? { sessionId: input.sessionId } : void 0
   );
 }
+function pushKindForNoun(noun) {
+  return noun === "Gap" ? "gap" : noun === "Issue" ? "issue" : "findings";
+}
 async function runMintIssue(flags, deps2) {
   try {
     let sessionId = null;
@@ -25135,9 +25234,10 @@ async function runMintIssue(flags, deps2) {
         issueKey: minted.key ?? null,
         boardId: board.id,
         artifactId: flags.artifact,
+        artifactLinked: minted.artifactLinked,
         relatedTaskId: flags.fromTask,
         linkKind: flags.blocks ? "BLOCKS" : "RELATES_TO"
-      }) : `Minted ${minted.key ?? minted.id} on ${board.name} \xB7 artifact linked \xB7 ${flags.blocks ? "BLOCKS" : "RELATES_TO"} ${flags.fromTask}`
+      }) : `Minted ${minted.key ?? minted.id} on ${board.name} \xB7 ${minted.artifactLinked ? "artifact linked" : "artifact NOT linked (see note)"} \xB7 ${flags.blocks ? "BLOCKS" : "RELATES_TO"} ${flags.fromTask}`
     );
     return 0;
   } catch (error2) {
@@ -26020,28 +26120,6 @@ function cellText(value) {
   return text;
 }
 
-// src/retry.ts
-async function withRateLimitRetry(fn, options) {
-  const { maxRetries, maxWaitSeconds, sleep, now } = options;
-  const start = now();
-  let attempt = 0;
-  for (; ; ) {
-    const result = await fn();
-    const envelope = envelopeOfResult(result);
-    if (envelope?.error.code !== "RATE_LIMITED") return result;
-    const retryAfter = envelope.error.retryAfterSeconds;
-    if (typeof retryAfter !== "number" || !Number.isFinite(retryAfter)) {
-      return result;
-    }
-    if (retryAfter < 0) return result;
-    if (attempt >= maxRetries) return result;
-    const elapsedMs = now() - start;
-    if (elapsedMs + retryAfter * 1e3 > maxWaitSeconds * 1e3) return result;
-    await sleep(retryAfter * 1e3);
-    attempt += 1;
-  }
-}
-
 // src/call.ts
 async function callTool(client, name, args, options) {
   let result;
@@ -27577,7 +27655,10 @@ function renderOperatorIdentity(operator, workspaceName) {
 }
 async function executable(path) {
   try {
-    await fs.access(path, constants.X_OK);
+    await fs.access(
+      path,
+      process.platform === "win32" ? constants.F_OK : constants.X_OK
+    );
     return await fs.realpath(path);
   } catch {
     return null;
@@ -28302,8 +28383,15 @@ async function runSetupCommand(flags, deps2) {
   }
   const codex = await deps2.resolveCodex();
   if (codex) await registerCodexMcp(deps2, codex, pending);
-  if (flags.git !== false && deps2.isInteractive && deps2.cwd() !== deps2.homeDir()) {
-    await bootstrapRepository(deps2);
+  if (flags.git !== false && deps2.cwd() !== deps2.homeDir()) {
+    if (deps2.isInteractive) {
+      await bootstrapRepository(deps2);
+    } else if (!await deps2.resolveGit() || (await deps2.git(["rev-parse", "--is-inside-work-tree"], deps2.cwd())).code !== 0) {
+      say(
+        deps2,
+        "note: skipped the repository offer (not an interactive terminal) \u2014 this folder is not a git work tree, and align requires one. Run `git init` here first."
+      );
+    }
   }
   say(deps2, "");
   if (pending.failedPlugins.length) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jentrix/cli",
-  "version": "0.5.12",
+  "version": "0.5.13",
   "description": "Command-line client for the Jentrix MCP surface (jentrix tool <name>, generated noun-verb commands).",
   "keywords": [
     "jentrix",