sequant 1.15.1 → 1.15.2

package/.claude-plugin/marketplace.json

@@ -3,8 +3,8 @@
   "name": "sequant",
   "description": "Sequant plugin marketplace - structured workflow system for Claude Code",
   "owner": {
-    "name": "admarble",
-    "email": "github@admarble.com"
+    "name": "sequant-io",
+    "email": "hello@sequant.io"
   },
   "plugins": [
     {
@@ -12,8 +12,8 @@
       "description": "Structured workflow system for Claude Code - GitHub issue resolution with spec, exec, test, and QA phases. Includes 16 skills for planning, implementation, testing, code review, and quality assurance.",
       "version": "1.13.0",
       "author": {
-        "name": "admarble",
-        "email": "github@admarble.com"
+        "name": "sequant-io",
+        "email": "hello@sequant.io"
       },
       "source": "./",
       "category": "workflow"

package/.claude-plugin/plugin.json

@@ -1,9 +1,9 @@
 {
   "name": "sequant",
   "description": "Structured workflow system for Claude Code - GitHub issue resolution with spec, exec, test, and QA phases",
-  "version": "1.15.1",
+  "version": "1.15.2",
   "author": {
-    "name": "admarble",
-    "email": "github@admarble.com"
+    "name": "sequant-io",
+    "email": "hello@sequant.io"
   }
 }

package/README.md

@@ -238,9 +238,9 @@ Stack guides: [Next.js](docs/stacks/nextjs.md) · [Rust](docs/stacks/rust.md) ·
 
 ### Reporting Issues
 
-- **Bug reports:** [Bug template](https://github.com/admarble/sequant/issues/new?template=bug.yml)
-- **Feature requests:** [Feature template](https://github.com/admarble/sequant/issues/new?template=feature.yml)
-- **Questions:** [GitHub Discussions](https://github.com/admarble/sequant/discussions)
+- **Bug reports:** [Bug template](https://github.com/sequant-io/sequant/issues/new?template=bug.yml)
+- **Feature requests:** [Feature template](https://github.com/sequant-io/sequant/issues/new?template=feature.yml)
+- **Questions:** [GitHub Discussions](https://github.com/sequant-io/sequant/discussions)
 
 ### Using `/improve` for Feedback
 

package/dist/src/commands/init.js

@@ -407,5 +407,5 @@ export async function initCommand(options) {
     if (optionalSection) {
         console.log(optionalSection);
     }
-    console.log(chalk.gray("\nDocumentation: https://github.com/admarble/sequant#readme\n"));
+    console.log(chalk.gray("\nDocumentation: https://github.com/sequant-io/sequant#readme\n"));
 }

package/dist/src/commands/run.js

@@ -201,6 +201,47 @@ async function ensureWorktree(issueNumber, title, verbose, packageManager, baseB
         if (verbose) {
             console.log(chalk.gray(`    📂 Reusing existing worktree: ${existingPath}`));
         }
+        // In chain mode, rebase existing worktree onto previous chain link
+        if (chainMode && baseBranch) {
+            if (verbose) {
+                console.log(chalk.gray(`    🔄 Rebasing existing worktree onto chain base (${baseBranch})...`));
+            }
+            const rebaseResult = spawnSync("git", ["-C", existingPath, "rebase", baseBranch], { stdio: "pipe" });
+            if (rebaseResult.status !== 0) {
+                const rebaseError = rebaseResult.stderr.toString();
+                // Check if it's a conflict
+                if (rebaseError.includes("CONFLICT") ||
+                    rebaseError.includes("could not apply")) {
+                    console.log(chalk.yellow(`    ⚠️  Rebase conflict detected. Aborting rebase and keeping original branch state.`));
+                    console.log(chalk.yellow(`    ℹ️  Branch ${branch} is not properly chained. Manual rebase may be required.`));
+                    // Abort the rebase to restore branch state
+                    spawnSync("git", ["-C", existingPath, "rebase", "--abort"], {
+                        stdio: "pipe",
+                    });
+                }
+                else {
+                    console.log(chalk.yellow(`    ⚠️  Rebase failed: ${rebaseError.trim()}`));
+                    console.log(chalk.yellow(`    ℹ️  Continuing with branch in its original state.`));
+                }
+                return {
+                    issue: issueNumber,
+                    path: existingPath,
+                    branch,
+                    existed: true,
+                    rebased: false,
+                };
+            }
+            if (verbose) {
+                console.log(chalk.green(`    ✅ Existing worktree rebased onto ${baseBranch}`));
+            }
+            return {
+                issue: issueNumber,
+                path: existingPath,
+                branch,
+                existed: true,
+                rebased: true,
+            };
+        }
         return {
             issue: issueNumber,
             path: existingPath,
@@ -444,9 +485,7 @@ export function createCheckpointCommit(worktreePath, issueNumber, verbose) {
     const commitMessage = `checkpoint(#${issueNumber}): QA passed
 
 This is an automatic checkpoint commit created after issue #${issueNumber}
-passed QA in chain mode. It serves as a recovery point if later issues fail.
-
-Co-Authored-By: Sequant <noreply@sequant.dev>`;
+passed QA in chain mode. It serves as a recovery point if later issues fail.`;
     const commitResult = spawnSync("git", ["-C", worktreePath, "commit", "-m", commitMessage], { stdio: "pipe" });
     if (commitResult.status !== 0) {
         const error = commitResult.stderr.toString();
@@ -671,6 +710,11 @@ async function executePhase(issueNumber, phase, config, sessionId, worktreePath,
         // Get MCP servers config if enabled
         // Reads from Claude Desktop config and passes to SDK for headless MCP support
         const mcpServers = config.mcp ? getMcpServersConfig() : undefined;
+        // Track whether we're actively streaming verbose output
+        // Pausing spinner once per streaming session prevents truncation from rapid pause/resume cycles
+        // (Issue #283: ora's stop() clears the current line, which can truncate output when
+        // pause/resume is called for every chunk in rapid succession)
+        let verboseStreamingActive = false;
         const queryInstance = query({
             prompt,
             options: {
@@ -693,10 +737,14 @@ async function executePhase(issueNumber, phase, config, sessionId, worktreePath,
                 // Capture stderr for debugging (helps diagnose early exit failures)
                 stderr: (data) => {
                     capturedStderr += data;
+                    // Write stderr in verbose mode
                     if (config.verbose) {
-                        spinner?.pause();
+                        // Pause spinner once to avoid truncation (Issue #283)
+                        if (!verboseStreamingActive) {
+                            spinner?.pause();
+                            verboseStreamingActive = true;
+                        }
                         process.stderr.write(chalk.red(data));
-                        spinner?.resume();
                     }
                 },
             },
@@ -719,10 +767,13 @@ async function executePhase(issueNumber, phase, config, sessionId, worktreePath,
                     capturedOutput += textContent;
                     // Show streaming output in verbose mode
                     if (config.verbose) {
-                        // Pause spinner during verbose streaming to avoid terminal corruption
-                        spinner?.pause();
+                        // Pause spinner once at start of streaming to avoid truncation
+                        // (Issue #283: repeated pause/resume causes ora to clear lines between chunks)
+                        if (!verboseStreamingActive) {
+                            spinner?.pause();
+                            verboseStreamingActive = true;
+                        }
                         process.stdout.write(chalk.gray(textContent));
-                        spinner?.resume();
                     }
                 }
             }
@@ -731,6 +782,11 @@ async function executePhase(issueNumber, phase, config, sessionId, worktreePath,
                 resultMessage = message;
             }
         }
+        // Resume spinner after streaming completes (if we paused it)
+        if (verboseStreamingActive) {
+            spinner?.resume();
+            verboseStreamingActive = false;
+        }
         clearTimeout(timeoutId);
         // Clear abort controller from shutdown manager
         if (shutdownManager) {
@@ -1190,6 +1246,8 @@ export async function runCommand(issues, options) {
             sequential: config.sequential,
             qualityLoop: config.qualityLoop,
             maxIterations: config.maxIterations,
+            chain: mergedOptions.chain,
+            qaGate: mergedOptions.qaGate,
         };
         logWriter = new LogWriter({
             logPath: mergedOptions.logPath ?? settings.run.logPath,

package/dist/src/lib/upstream/issues.js

@@ -57,7 +57,7 @@ async function execCommand(command, args) {
 /**
  * Check if a similar upstream issue already exists
  */
-export async function checkForDuplicate(title, owner = "admarble", repo = "sequant") {
+export async function checkForDuplicate(title, owner = "sequant-io", repo = "sequant") {
     try {
         validateRepoParams(owner, repo);
         // Search for existing upstream issues with similar title
@@ -152,7 +152,7 @@ export function isSimilarTitle(title1, title2) {
  * Create a GitHub issue using a temporary file for the body
  * This avoids any shell escaping issues with complex markdown content
  */
-export async function createIssue(params, owner = "admarble", repo = "sequant") {
+export async function createIssue(params, owner = "sequant-io", repo = "sequant") {
     validateRepoParams(owner, repo);
     // Write body to a temp file to avoid any escaping issues
     const tempFile = join(tmpdir(), `gh-issue-body-${Date.now()}.md`);
@@ -193,7 +193,7 @@ export async function createIssue(params, owner = "admarble", repo = "sequant")
 /**
  * Add a comment to an existing issue
  */
-export async function addIssueComment(issueNumber, comment, owner = "admarble", repo = "sequant") {
+export async function addIssueComment(issueNumber, comment, owner = "sequant-io", repo = "sequant") {
     validateRepoParams(owner, repo);
     // Validate issue number
     if (!Number.isInteger(issueNumber) || issueNumber < 1) {
@@ -226,7 +226,7 @@ export async function addIssueComment(issueNumber, comment, owner = "admarble",
 /**
  * Create or link an issue for a finding
  */
-export async function createOrLinkFinding(finding, version, assessmentIssueNumber, dryRun = false, owner = "admarble", repo = "sequant") {
+export async function createOrLinkFinding(finding, version, assessmentIssueNumber, dryRun = false, owner = "sequant-io", repo = "sequant") {
     // Generate issue content
     const issueContent = generateFindingIssue(finding, version, assessmentIssueNumber);
     // Check for duplicate
@@ -254,7 +254,7 @@ export async function createOrLinkFinding(finding, version, assessmentIssueNumbe
 /**
  * Create the assessment summary issue
  */
-export async function createAssessmentIssue(title, body, dryRun = false, owner = "admarble", repo = "sequant") {
+export async function createAssessmentIssue(title, body, dryRun = false, owner = "sequant-io", repo = "sequant") {
     if (dryRun) {
         return undefined;
     }

package/dist/src/lib/workflow/run-log-schema.d.ts

@@ -157,6 +157,8 @@ export declare const RunConfigSchema: z.ZodObject<{
     sequential: z.ZodBoolean;
     qualityLoop: z.ZodBoolean;
     maxIterations: z.ZodNumber;
+    chain: z.ZodOptional<z.ZodBoolean>;
+    qaGate: z.ZodOptional<z.ZodBoolean>;
 }, z.core.$strip>;
 export type RunConfig = z.infer<typeof RunConfigSchema>;
 /**
@@ -192,6 +194,8 @@ export declare const RunLogSchema: z.ZodObject<{
         sequential: z.ZodBoolean;
         qualityLoop: z.ZodBoolean;
         maxIterations: z.ZodNumber;
+        chain: z.ZodOptional<z.ZodBoolean>;
+        qaGate: z.ZodOptional<z.ZodBoolean>;
     }, z.core.$strip>;
     issues: z.ZodArray<z.ZodObject<{
         issueNumber: z.ZodNumber;

package/dist/src/lib/workflow/run-log-schema.js

@@ -109,6 +109,10 @@ export const RunConfigSchema = z.object({
     qualityLoop: z.boolean(),
     /** Maximum iterations for fix loops */
     maxIterations: z.number().int().positive(),
+    /** Whether chain mode was enabled (each issue branches from previous) */
+    chain: z.boolean().optional(),
+    /** Whether QA gate was enabled (chain pauses if QA fails) */
+    qaGate: z.boolean().optional(),
 });
 /**
  * Summary statistics for a run

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "sequant",
-  "version": "1.15.1",
+  "version": "1.15.2",
   "description": "Quantize your development workflow - Sequential AI phases with quality gates",
   "type": "module",
   "bin": {
@@ -45,12 +45,12 @@
   "license": "MIT",
   "repository": {
     "type": "git",
-    "url": "git+https://github.com/admarble/sequant.git"
+    "url": "git+https://github.com/sequant-io/sequant.git"
   },
   "bugs": {
-    "url": "https://github.com/admarble/sequant/issues"
+    "url": "https://github.com/sequant-io/sequant/issues"
   },
-  "homepage": "https://github.com/admarble/sequant#readme",
+  "homepage": "https://github.com/sequant-io/sequant#readme",
   "engines": {
     "node": ">=18.0.0"
   },

package/templates/skills/qa/SKILL.md

@@ -369,7 +369,7 @@ fi
 
 **If no verification evidence exists:**
 1. Prompt: "Script changes detected but no execution verification found. Run `/verify <issue> --command \"<test command>\"` before READY_FOR_MERGE verdict."
-2. Do NOT give `READY_FOR_MERGE` verdict until verification is complete
+2. Do NOT give `READY_FOR_MERGE` verdict until verification is complete (unless an approved override applies — see Section 9a)
 3. Verdict should be `AC_MET_BUT_NOT_A_PLUS` with note about missing verification
 
 **Why this matters:**
@@ -389,6 +389,59 @@ fi
 /qa 558  # Re-run, now sees verification, can give READY_FOR_MERGE
 ```
 
+### 9a. Script Verification Override
+
+In some cases, `/verify` execution can be safely skipped when script changes are purely cosmetic or have no runtime impact. **Overrides require explicit justification and risk assessment.**
+
+**Override Format (REQUIRED when skipping /verify):**
+
+```markdown
+### Script Verification Override
+
+**Requirement:** `/verify` before READY_FOR_MERGE
+**Override:** Yes
+**Justification:** [One of the approved categories below]
+**Risk Assessment:** [None/Low/Medium]
+```
+
+**Approved Override Categories:**
+
+| Category | Example | Risk |
+|----------|---------|------|
+| Syntax-only refactor | `catch (error)` → `catch` | None |
+| Comment/documentation changes | Adding JSDoc, updating comments | None |
+| Type annotation additions | Adding `: string`, `: number` | None |
+| Import reorganization | Sorting imports, removing unused | None |
+| Variable rename (no logic change) | `foo` → `bar` with no behavioral change | Low |
+| Dead code removal | Removing unreachable branches | Low |
+
+**NOT Approved for Override (always require /verify):**
+
+| Category | Example | Why |
+|----------|---------|-----|
+| Logic changes | Modified conditionals, new branches | Runtime behavior changes |
+| New functionality | Added functions, new exports | Must verify execution |
+| Dependency changes | Updated imports from new packages | May affect runtime |
+| Error handling changes | Modified catch blocks, new try/catch | Failure paths change |
+| Configuration changes | Modified env vars, config parsing | Environment-dependent |
+
+**Risk Assessment Definitions:**
+
+| Level | Meaning | Criteria |
+|-------|---------|----------|
+| **None** | Zero runtime impact | Change is invisible at runtime (comments, types, syntax) |
+| **Low** | Negligible runtime impact | Change is cosmetic (rename, dead code) with no logical effect |
+| **Medium** | Possible runtime impact | Change touches executable code but appears safe — **should NOT be overridden** |
+
+**Override Decision Flow:**
+
+1. Check if change matches an approved category → If no, `/verify` is required
+2. Assess risk level → If Medium or higher, `/verify` is required
+3. Document override using the format above in the QA output
+4. Include override in the GitHub issue comment for audit trail
+
+**CRITICAL:** When in doubt, run `/verify`. Overrides are for clear-cut cases only. If you need to argue that a change is safe, it probably needs verification.
+
 ---
 
 ## Output Verification
@@ -399,6 +452,7 @@ fi
 - [ ] **Verdict** - One of: READY_FOR_MERGE, AC_MET_BUT_NOT_A_PLUS, AC_NOT_MET
 - [ ] **Quality Metrics** - Type issues, deleted tests, files changed, additions/deletions
 - [ ] **Code Review Findings** - Strengths, issues, suggestions
+- [ ] **Script Verification Override** - Included if scripts/CLI modified AND /verify was skipped (with justification and risk assessment)
 - [ ] **Documentation Check** - README/docs updated if feature adds new functionality
 - [ ] **Next Steps** - Clear, actionable recommendations
 
@@ -447,6 +501,17 @@ You MUST include these sections:
 
 ---
 
+### Script Verification Override
+
+[Include if scripts/CLI modified AND /verify was skipped, otherwise omit this section]
+
+**Requirement:** `/verify` before READY_FOR_MERGE
+**Override:** Yes
+**Justification:** [Approved category from Section 9a]
+**Risk Assessment:** [None/Low/Medium]
+
+---
+
 ### Verdict: [READY_FOR_MERGE | AC_MET_BUT_NOT_A_PLUS | AC_NOT_MET]
 
 [Explanation of verdict]