gsd-pi 2.78.0 → 2.78.1-dev.9d08d820b

package/dist/resources/extensions/gsd/commands/catalog.js

@@ -1,10 +1,9 @@
 import { existsSync, readFileSync, readdirSync } from "node:fs";
 import { homedir } from "node:os";
-import { join } from "node:path";
+import { join, resolve } from "node:path";
 import { loadRegistry } from "../workflow-templates.js";
-import { resolveProjectRoot } from "../worktree.js";
 const gsdHome = process.env.GSD_HOME || join(homedir(), ".gsd");
-export const GSD_COMMAND_DESCRIPTION = "GSD — Get Shit Done: /gsd help|start|templates|next|auto|stop|pause|status|widget|visualize|queue|quick|discuss|capture|triage|dispatch|history|undo|undo-task|reset-slice|rate|skip|export|cleanup|model|mode|prefs|config|keys|hooks|run-hook|skill-health|doctor|debug|logs|forensics|changelog|migrate|remote|steer|knowledge|new-milestone|parallel|cmux|park|unpark|init|setup|onboarding|inspect|extensions|update|fast|mcp|rethink|codebase|notifications|ship|do|session-report|backlog|pr-branch|add-tests|scan|language";
+export const GSD_COMMAND_DESCRIPTION = "GSD — Get Shit Done: /gsd help|start|templates|next|auto|stop|pause|status|widget|visualize|queue|quick|discuss|capture|triage|dispatch|history|undo|undo-task|reset-slice|rate|skip|export|cleanup|model|mode|prefs|config|keys|hooks|run-hook|skill-health|doctor|debug|logs|forensics|changelog|migrate|remote|steer|knowledge|new-milestone|parallel|cmux|park|unpark|init|setup|onboarding|inspect|extensions|update|fast|mcp|rethink|workflow|codebase|notifications|ship|do|session-report|backlog|pr-branch|add-tests|scan|language";
 export const TOP_LEVEL_SUBCOMMANDS = [
     { cmd: "help", desc: "Categorized command reference with descriptions" },
     { cmd: "next", desc: "Explicit step mode (same as /gsd)" },
@@ -330,6 +329,71 @@ function getExtensionCompletions(prefix, action) {
         return [];
     }
 }
+function normalizePathForCompare(path) {
+    return path.replaceAll("\\", "/").replace(/\/+$/, "");
+}
+function findWorktreeSegment(normalizedPath) {
+    const directMarker = "/.gsd/worktrees/";
+    const directIdx = normalizedPath.indexOf(directMarker);
+    if (directIdx !== -1) {
+        return { gsdIdx: directIdx, afterWorktrees: directIdx + directMarker.length };
+    }
+    const symlinkMatch = normalizedPath.match(/\/\.gsd\/projects\/[a-f0-9]+\/worktrees\//);
+    if (symlinkMatch?.index !== undefined) {
+        return { gsdIdx: symlinkMatch.index, afterWorktrees: symlinkMatch.index + symlinkMatch[0].length };
+    }
+    return null;
+}
+function resolveProjectRootFromGitFile(worktreePath) {
+    try {
+        let dir = worktreePath;
+        for (let i = 0; i < 30; i++) {
+            const gitPath = join(dir, ".git");
+            if (existsSync(gitPath)) {
+                const content = readFileSync(gitPath, "utf8").trim();
+                if (content.startsWith("gitdir: ")) {
+                    const gitDir = resolve(dir, content.slice(8));
+                    const dotGitDir = resolve(gitDir, "..", "..");
+                    if (dotGitDir.endsWith(".git") || dotGitDir.endsWith(".git/") || dotGitDir.endsWith(".git\\")) {
+                        return resolve(dotGitDir, "..");
+                    }
+                    const commonDirPath = join(gitDir, "commondir");
+                    if (existsSync(commonDirPath)) {
+                        const commonDir = readFileSync(commonDirPath, "utf8").trim();
+                        return resolve(resolve(gitDir, commonDir), "..");
+                    }
+                }
+                break;
+            }
+            const parent = resolve(dir, "..");
+            if (parent === dir)
+                break;
+            dir = parent;
+        }
+    }
+    catch {
+        // Completion must stay best-effort.
+    }
+    return null;
+}
+function resolveProjectRootForCompletion(basePath) {
+    if (process.env.GSD_PROJECT_ROOT)
+        return process.env.GSD_PROJECT_ROOT;
+    const normalizedPath = normalizePathForCompare(basePath);
+    const segment = findWorktreeSegment(normalizedPath);
+    if (!segment)
+        return basePath;
+    const separator = basePath.includes("\\") ? "\\" : "/";
+    const gsdMarker = `${separator}.gsd${separator}`;
+    const gsdIdx = basePath.indexOf(gsdMarker);
+    const candidate = gsdIdx !== -1 ? basePath.slice(0, gsdIdx) : basePath.slice(0, segment.gsdIdx);
+    const normalizedGsdHome = normalizePathForCompare(gsdHome);
+    const candidateGsdPath = normalizePathForCompare(join(candidate, ".gsd"));
+    if (candidateGsdPath === normalizedGsdHome || candidateGsdPath.startsWith(`${normalizedGsdHome}/`)) {
+        return resolveProjectRootFromGitFile(basePath) ?? basePath;
+    }
+    return candidate;
+}
 export function getGsdArgumentCompletions(prefix) {
     const hasTrailingSpace = prefix.endsWith(" ");
     const parts = prefix.trim().split(/\s+/);
@@ -384,7 +448,7 @@ export function getGsdArgumentCompletions(prefix) {
     // Workflow definition-name completion for `workflow run <name>` and `workflow validate <name>`
     if (command === "workflow" && (subcommand === "run" || subcommand === "validate") && parts.length <= 3) {
         try {
-            const defsDir = join(resolveProjectRoot(process.cwd()), ".gsd", "workflow-defs");
+            const defsDir = join(resolveProjectRootForCompletion(process.cwd()), ".gsd", "workflow-defs");
             if (existsSync(defsDir)) {
                 return readdirSync(defsDir)
                     .filter((f) => f.endsWith(".yaml") && f.startsWith(third))
@@ -426,7 +490,7 @@ export function getGsdArgumentCompletions(prefix) {
             catch { /* ignore */ }
         };
         try {
-            const base = resolveProjectRoot(process.cwd());
+            const base = resolveProjectRootForCompletion(process.cwd());
             scanDir(join(base, ".gsd", "workflows"), "project");
             scanDir(join(base, ".gsd", "workflow-defs"), "project-legacy");
             scanDir(join(gsdHome, "workflows"), "global");

package/dist/resources/extensions/gsd/commands/handlers/core.js

@@ -58,16 +58,21 @@ export function showHelp(ctx, args = "") {
         "  /gsd pause          Pause auto-mode (preserves state, /gsd auto to resume)",
         "  /gsd discuss        Start guided milestone/slice discussion",
         "  /gsd new-milestone  Create milestone from headless context (used by gsd headless)",
+        "  /gsd quick          Execute a quick task without full planning overhead",
+        "  /gsd dispatch       Dispatch a specific phase directly  [research|plan|execute|complete|uat|replan]",
+        "  /gsd parallel       Parallel milestone orchestration  [start|status|stop|pause|resume|merge|watch]",
+        "  /gsd workflow       Custom workflow lifecycle  [new|run|list|validate|pause|resume]",
         "",
         "VISIBILITY",
         `  /gsd status         Show progress dashboard  (${formattedShortcutPair("dashboard")})`,
         `  /gsd parallel watch Open parallel worker monitor  (${formattedShortcutPair("parallel")})`,
+        "  /gsd widget         Cycle status widget  [full|small|min|off]",
         "  /gsd visualize      Interactive 10-tab TUI (progress, timeline, deps, metrics, health, agent, changes, knowledge, captures, export)",
         "  /gsd queue          Show queued/dispatched units and execution order",
         "  /gsd history        View execution history  [--cost] [--phase] [--model] [N]",
         "  /gsd changelog      Show categorized release notes  [version]",
         `  /gsd notifications  View persistent notification history  [clear|tail|filter]  (${formattedShortcutPair("notifications")})`,
-        "  /gsd logs           Browse activity logs, debug logs, and metrics",
+        "  /gsd logs           Browse activity logs, debug logs, and metrics  [debug|tail|clear]",
         "  /gsd debug          Create/list/continue persistent debug sessions",
         "",
         "COURSE CORRECTION",
@@ -76,6 +81,9 @@ export function showHelp(ctx, args = "") {
         "  /gsd triage         Classify and route pending captures",
         "  /gsd skip <unit>    Prevent a unit from auto-mode dispatch",
         "  /gsd undo           Revert last completed unit  [--force]",
+        "  /gsd undo-task      Reset a specific task's completion state  [DB + markdown]",
+        "  /gsd reset-slice    Reset a slice and all its tasks  [DB + markdown]",
+        "  /gsd rate           Rate last unit's model tier  [over|ok|under]",
         "  /gsd rethink        Conversational project reorganization — reorder, park, discard, add milestones",
         "  /gsd park [id]      Park a milestone — skip without deleting  [reason]",
         "  /gsd unpark [id]    Reactivate a parked milestone",
@@ -84,6 +92,15 @@ export function showHelp(ctx, args = "") {
         "  /gsd knowledge <type> <text>   Add rule, pattern, or lesson to KNOWLEDGE.md",
         "  /gsd codebase [generate|update|stats]   Manage the CODEBASE.md cache used in prompt context",
         "",
+        "SHIPPING & BACKLOG",
+        "  /gsd ship           Create a PR from milestone artifacts  [--dry-run|--draft|--base|--force]",
+        "  /gsd do <text>      Route freeform text to the right GSD command",
+        "  /gsd session-report Show session cost, tokens, and work summary  [--json|--save]",
+        "  /gsd backlog        Manage backlog items  [add|promote|remove|list]",
+        "  /gsd pr-branch      Create a clean PR branch filtering .gsd/ commits  [--dry-run|--name]",
+        "  /gsd add-tests      Generate tests for completed slices",
+        "  /gsd scan           Rapid codebase assessment  [--focus tech|arch|quality|concerns|tech+arch]",
+        "",
         "SETUP & CONFIGURATION",
         "  /gsd onboarding     Re-run setup wizard  [--resume|--reset|--step <name>]",
         "  /gsd setup          Configuration hub  [llm|model|search|remote|keys|prefs|onboarding]",
@@ -96,18 +113,22 @@ export function showHelp(ctx, args = "") {
         "  /gsd config         (deprecated) Set tool API keys — use /gsd keys instead",
         "  /gsd show-config    Show effective configuration (models, routing, toggles)",
         "  /gsd hooks          Show post-unit hook configuration",
+        "  /gsd run-hook       Manually trigger a specific hook",
+        "  /gsd skill-health   Skill lifecycle dashboard",
         "  /gsd extensions     Manage extensions  [list|enable|disable|info]",
         "  /gsd fast           Toggle OpenAI service tier  [on|off|flex|status]",
         "  /gsd mcp            MCP server status and connectivity  [status|check <server>|init [dir]]",
         "",
         "MAINTENANCE",
         "  /gsd doctor         Diagnose and repair .gsd/ state  [audit|fix|heal] [scope]",
+        "  /gsd forensics      Examine execution logs and post-mortem analysis",
         "  /gsd export         Export milestone/slice results  [--json|--markdown|--html] [--all]",
         "  /gsd cleanup        Remove merged branches or snapshots  [branches|snapshots]",
         "  /gsd migrate        Migrate .planning/ (v1) to .gsd/ (v2) format",
         "  /gsd remote         Control remote auto-mode  [slack|discord|status|disconnect]",
         "  /gsd inspect        Show SQLite DB diagnostics (schema, row counts, recent entries)",
         "  /gsd update         Update GSD to the latest version via npm",
+        "  /gsd language       Set or clear the global response language  [off|clear|<language>]",
     ];
     const full = ["full", "--full", "all"].includes(args.trim().toLowerCase());
     ctx.ui.notify((full ? fullLines : summaryLines).join("\n"), "info");

package/dist/resources/extensions/gsd/commands-config.js

@@ -6,6 +6,7 @@
 import { AuthStorage } from "@gsd/pi-coding-agent";
 import { existsSync, mkdirSync } from "node:fs";
 import { join, dirname } from "node:path";
+import { getHomeDir } from "./home-dir.js";
 /**
  * Tool API key configurations.
  * This is the source of truth for tool credentials - used by both the config wizard
@@ -29,7 +30,7 @@ function getStoredToolKey(auth, providerId) {
  */
 export function loadToolApiKeys() {
     try {
-        const authPath = join(process.env.HOME ?? "", ".gsd", "agent", "auth.json");
+        const authPath = join(getHomeDir(), ".gsd", "agent", "auth.json");
         if (!existsSync(authPath))
             return;
         const auth = AuthStorage.create(authPath);
@@ -45,7 +46,7 @@ export function loadToolApiKeys() {
     }
 }
 export function getConfigAuthStorage() {
-    const authPath = join(process.env.HOME ?? "", ".gsd", "agent", "auth.json");
+    const authPath = join(getHomeDir(), ".gsd", "agent", "auth.json");
     mkdirSync(dirname(authPath), { recursive: true });
     return AuthStorage.create(authPath);
 }

package/dist/resources/extensions/gsd/commands-extensions.js

@@ -10,7 +10,50 @@ import { dirname, join, resolve } from "node:path";
 import { homedir, tmpdir } from "node:os";
 import { execFileSync } from "node:child_process";
 import { lockSync, unlockSync } from "proper-lockfile";
-import semver from "semver";
+/**
+ * Strict numeric comparison of two npm-style version strings.
+ *
+ * Returns true when `a` is strictly greater than `b`. Compares the dotted
+ * release components numerically (so `1.10.0` > `1.9.0`) and treats any
+ * prerelease suffix (`-beta.1`, `-rc.2`) as less than the equivalent
+ * release version (`1.0.0` > `1.0.0-beta.1`). Sufficient for npm package
+ * version comparison in the extension installer; we don't need the full
+ * semver range/intersect machinery here.
+ *
+ * Replaces the earlier `import semver from "semver"` — that import broke
+ * `tsc -p tsconfig.json` whenever `@types/semver` failed to install
+ * (Issue #4946) because the file is pulled in transitively despite being
+ * under the `src/resources` exclude.
+ */
+export function isVersionGreater(a, b) {
+    const split = (v) => {
+        const dash = v.indexOf("-");
+        const release = (dash === -1 ? v : v.slice(0, dash))
+            .split(".")
+            .map(part => Number.parseInt(part, 10) || 0);
+        const pre = dash === -1 ? null : v.slice(dash + 1);
+        return { release, pre };
+    };
+    const sa = split(a);
+    const sb = split(b);
+    const len = Math.max(sa.release.length, sb.release.length);
+    for (let i = 0; i < len; i++) {
+        const ai = sa.release[i] ?? 0;
+        const bi = sb.release[i] ?? 0;
+        if (ai !== bi)
+            return ai > bi;
+    }
+    // Release components equal — a release version beats any prerelease,
+    // and prerelease strings are compared lexicographically (good enough
+    // for `beta.1` vs `beta.2`, the only realistic case here).
+    if (sa.pre === null && sb.pre !== null)
+        return true;
+    if (sa.pre !== null && sb.pre === null)
+        return false;
+    if (sa.pre !== null && sb.pre !== null)
+        return sa.pre > sb.pre;
+    return false;
+}
 const gsdHome = process.env.GSD_HOME || join(homedir(), ".gsd");
 // ─── Registry I/O ───────────────────────────────────────────────────────────
 function getRegistryPath() {
@@ -413,7 +456,7 @@ async function updateSingleExtension(id, registry, ctx) {
         ctx.ui.notify(`Could not fetch latest version for "${id}".`, "warning");
         return;
     }
-    if (semver.gt(latest, current)) {
+    if (isVersionGreater(latest, current)) {
         ctx.ui.notify(`Updating "${id}": v${current} → v${latest}...`, "info");
         await handleInstall(packageName, ctx);
     }
@@ -464,7 +507,7 @@ async function updateAllExtensions(registry, ctx) {
             skipped++;
             continue;
         }
-        if (semver.gt(latest, current)) {
+        if (isVersionGreater(latest, current)) {
             ctx.ui.notify(`  ${entry.id}: v${current} → v${latest} (updating)`, "info");
             await handleInstall(packageName, ctx);
             updated++;

package/dist/resources/extensions/gsd/commands-handlers.js

@@ -9,6 +9,7 @@ import { join, resolve as resolvePath, sep } from "node:path";
 import { homedir } from "node:os";
 import { deriveState } from "./state.js";
 import { gsdRoot } from "./paths.js";
+import { getHomeDir } from "./home-dir.js";
 import { appendCapture, hasPendingCaptures, loadPendingCaptures } from "./captures.js";
 import { appendOverride, appendKnowledge } from "./files.js";
 import { formatDoctorIssuesForPrompt, formatDoctorReport, formatDoctorReportJson, runGSDDoctor, selectDoctorScope, filterDoctorIssues, } from "./doctor.js";
@@ -60,7 +61,7 @@ async function fetchLatestVersionForCommand() {
     }
 }
 export function dispatchDoctorHeal(pi, scope, reportText, structuredIssues) {
-    const workflowPath = process.env.GSD_WORKFLOW_PATH ?? join(process.env.HOME ?? "~", ".gsd", "agent", "GSD-WORKFLOW.md");
+    const workflowPath = process.env.GSD_WORKFLOW_PATH ?? join(getHomeDir(), ".gsd", "agent", "GSD-WORKFLOW.md");
     const workflow = readFileSync(workflowPath, "utf-8");
     const prompt = loadPrompt("doctor-heal", {
         doctorSummary: reportText,
@@ -210,7 +211,7 @@ export async function handleTriage(ctx, pi, basePath) {
         currentPlan: currentPlan || "(no active slice plan)",
         roadmapContext: roadmapContext || "(no active roadmap)",
     });
-    const workflowPath = process.env.GSD_WORKFLOW_PATH ?? join(process.env.HOME ?? "~", ".gsd", "agent", "GSD-WORKFLOW.md");
+    const workflowPath = process.env.GSD_WORKFLOW_PATH ?? join(getHomeDir(), ".gsd", "agent", "GSD-WORKFLOW.md");
     const workflow = readFileSync(workflowPath, "utf-8");
     pi.sendMessage({
         customType: "gsd-triage",

package/dist/resources/extensions/gsd/commands-mcp-status.js

@@ -10,6 +10,7 @@
  *   /gsd mcp init [dir]  — Write project-local GSD workflow MCP config
  */
 import { existsSync, readFileSync } from "node:fs";
+import { homedir } from "node:os";
 import { join, resolve } from "node:path";
 import { ensureProjectWorkflowMcpConfig } from "./mcp-project-config.js";
 export function formatMcpInitResult(status, configPath, targetPath) {
@@ -33,6 +34,7 @@ function readMcpConfigs() {
     const configPaths = [
         join(process.cwd(), ".mcp.json"),
         join(process.cwd(), ".gsd", "mcp.json"),
+        join(process.env.GSD_HOME || join(homedir(), ".gsd"), "mcp.json"),
     ];
     for (const configPath of configPaths) {
         try {
@@ -77,7 +79,7 @@ export function formatMcpStatusReport(servers) {
         return [
             "No MCP servers configured.",
             "",
-            "Add servers to .mcp.json or .gsd/mcp.json to enable MCP integrations.",
+            "Add servers to .mcp.json, .gsd/mcp.json, or $GSD_HOME/mcp.json (default: ~/.gsd/mcp.json) to enable MCP integrations.",
             "Tip: run /gsd mcp init . to write the local GSD workflow MCP config.",
             "See: https://modelcontextprotocol.io/quickstart",
         ].join("\n");

package/dist/resources/extensions/gsd/commands-prefs-wizard.js

@@ -1481,6 +1481,13 @@ async function configureAdvanced(ctx, prefs) {
     const tokenCost = await promptBoolean(ctx, "Show token cost in footer", prefs.show_token_cost, false);
     if (tokenCost !== undefined)
         prefs.show_token_cost = tokenCost;
+    const minRequestInterval = await promptInteger(ctx, "Minimum interval between auto-mode LLM requests (ms, 0 to disable)", prefs.min_request_interval_ms, "0");
+    if (minRequestInterval === "clear") {
+        delete prefs.min_request_interval_ms;
+    }
+    else if (minRequestInterval !== undefined) {
+        prefs.min_request_interval_ms = minRequestInterval;
+    }
     const widget = await promptEnum(ctx, "Auto-mode widget display", prefs.widget_mode, ["full", "small", "min", "off"], "full");
     if (widget !== undefined)
         prefs.widget_mode = widget;
@@ -1668,8 +1675,10 @@ export function serializePreferencesToFrontmatter(prefs) {
         "budget_ceiling", "budget_enforcement", "context_pause_threshold",
         "notifications", "cmux", "remote_questions", "git",
         "stale_commit_threshold_minutes",
+        "min_request_interval_ms",
         "post_unit_hooks", "pre_dispatch_hooks",
-        "dynamic_routing", "uok", "token_profile", "service_tier", "flat_rate_providers",
+        "dynamic_routing", "disabled_model_providers", "uok", "token_profile",
+        "service_tier", "flat_rate_providers",
         "phases", "parallel", "slice_parallel",
         "reactive_execution", "gate_evaluation",
         "auto_visualize", "auto_report",

package/dist/resources/extensions/gsd/dashboard-overlay.js

@@ -14,7 +14,7 @@ import { resolveMilestoneFile } from "./paths.js";
 import { getAutoDashboardData } from "./auto.js";
 import { getLedger, getProjectTotals, aggregateByPhase, aggregateBySlice, aggregateByModel, aggregateCacheHitRate, formatCost, formatTokenCount, formatCostProjection, } from "./metrics.js";
 import { loadEffectiveGSDPreferences } from "./preferences.js";
-import { getActiveWorktreeName } from "./worktree-command.js";
+import { getActiveWorktreeName } from "./worktree-session-state.js";
 import { getWorkerBatches, hasActiveWorkers } from "../subagent/worker-registry.js";
 import { formatDuration, padRight, joinColumns, centerLine, fitColumns, STATUS_GLYPH, STATUS_COLOR } from "../shared/mod.js";
 import { estimateTimeRemaining } from "./auto-dashboard.js";

package/dist/resources/extensions/gsd/docs/preferences-reference.md

@@ -126,6 +126,8 @@ Setting `prefer_skills: []` does **not** disable skill discovery — it just mea
   - `idle_timeout_minutes`: minutes of inactivity before the supervisor intervenes (default: 10).
   - `hard_timeout_minutes`: minutes before the supervisor forces termination (default: 30).
 
+- `min_request_interval_ms`: number — minimum integer milliseconds between auto-mode LLM request dispatches. Non-integer values are rounded down (e.g., `1000.9 → 1000`). Use this to proactively slow auto-mode on rate-limited providers and reduce 429 errors. Set to `0` to disable. Default: `0` (disabled).
+
 - `git`: configures GSD's git behavior. All fields are optional — omit any to use defaults. Keys:
   - `auto_push`: boolean — automatically push commits to the remote after committing. Default: `false`.
   - `push_branches`: boolean — push the milestone branch to the remote after commits. Default: `false`.
@@ -163,6 +165,12 @@ Setting `prefer_skills: []` does **not** disable skill discovery — it just mea
   - `skip_reassess`: boolean — force-disable roadmap reassessment even if `reassess_after_slice` is enabled. Default: `false`.
   - `skip_slice_research`: boolean — skip per-slice research. Default: `false`.
 
+- `reactive_execution`: controls automatic parallel task dispatch inside a slice. Reactive execution is enabled by default when omitted; set `enabled: false` to opt out. With default-on behavior, GSD only attempts a reactive batch when at least three ready tasks are available and the task-plan IO graph is non-ambiguous. If you set `enabled: true` explicitly, GSD uses the earlier opt-in threshold of two ready tasks. Keys:
+  - `enabled`: boolean — set `false` to force sequential task execution. Default: `true`.
+  - `max_parallel`: number — maximum tasks to dispatch in one batch, range `1`-`8`. Default: `2`.
+  - `isolation_mode`: `"same-tree"` — currently the only supported value.
+  - `subagent_model`: string — optional model override for reactive task subagents. Falls back to the `models.subagent` routing when omitted.
+
 - `remote_questions`: route interactive questions to Slack/Discord for headless auto-mode. Keys:
   - `channel`: `"slack"` or `"discord"` — channel type.
   - `channel_id`: string or number — channel ID.
@@ -193,6 +201,8 @@ Setting `prefer_skills: []` does **not** disable skill discovery — it just mea
   - `hooks`: boolean — enable routing hooks. Default: `true`.
   - `capability_routing`: boolean — enable capability-profile scoring for model selection within a tier. Requires `enabled: true`. Default: `false`.
 
+- `disabled_model_providers`: string[] — provider IDs to hide from model selection and routing (for example `["google-gemini-cli"]`). This only affects model availability (`/model`, auto-model selection, routing); it does not disable tool auth flows like `google_search`.
+
 - `uok`: Unified Orchestration Kernel controls. Keys:
   - `enabled`: boolean — enable kernel wrappers and contract observers. Default: `true`.
   - `legacy_fallback.enabled`: boolean — emergency release fallback that forces legacy orchestration behavior even when `uok.enabled` is `true`. Default: `false`.

package/dist/resources/extensions/gsd/doctor-providers.js

@@ -16,6 +16,7 @@ import { AuthStorage } from "@gsd/pi-coding-agent";
 import { getEnvApiKey } from "@gsd/pi-ai";
 import { loadEffectiveGSDPreferences } from "./preferences.js";
 import { getAuthPath, PROVIDER_REGISTRY } from "./key-manager.js";
+import { getHomeDir } from "./home-dir.js";
 // ── Provider routing constants ────────────────────────────────────────────────
 /**
  * Providers that use external CLI authentication (not API keys).
@@ -158,7 +159,7 @@ function isCliBinaryInPath(providerId) {
     return pathDirs.some(dir => executableNames.some(name => existsSync(join(dir, name))));
 }
 function modelsJsonPaths() {
-    const home = process.env.HOME ?? "~";
+    const home = getHomeDir();
     return [
         join(home, ".gsd", "agent", "models.json"),
         // Keep parity with custom-provider discovery during auto bootstrap.

package/dist/resources/extensions/gsd/doctor-runtime-checks.js

@@ -2,7 +2,7 @@ import { existsSync, lstatSync, readdirSync, readFileSync, realpathSync, rmSync,
 import { basename, dirname, join } from "node:path";
 import { cleanNumberedGsdVariants } from "./repo-identity.js";
 import { milestonesDir, gsdRoot, resolveGsdRootFile } from "./paths.js";
-import { deriveState } from "./state.js";
+import { deriveState, isGhostMilestone, isReusableGhostMilestone } from "./state.js";
 import { saveFile } from "./files.js";
 import { nativeIsRepo, nativeForEachRef, nativeUpdateRef } from "./native-git-bridge.js";
 import { readCrashLock, isLockProcessAlive, clearLock } from "./crash-recovery.js";
@@ -10,6 +10,7 @@ import { ensureGitignore, isGsdGitignored } from "./gitignore.js";
 import { readAllSessionStatuses, isSessionStale, removeSessionStatus } from "./session-status-io.js";
 import { recoverFailedMigration } from "./migrate-external.js";
 import { splitCompletedKey } from "./forensics.js";
+import { findMilestoneIds } from "./milestone-ids.js";
 export async function checkRuntimeHealth(basePath, issues, fixesApplied, shouldFix) {
     const root = gsdRoot(basePath);
     // ── Stale crash lock ──────────────────────────────────────────────────
@@ -570,6 +571,43 @@ export async function checkRuntimeHealth(basePath, issues, fixesApplied, shouldF
     catch {
         // Non-fatal — snapshot ref check failed
     }
+    // ── Orphan milestone directories (#4996) ──────────────────────────────
+    // Walk every milestone ID on disk. Any dir that has no DB row, no worktree,
+    // and no content files is an orphaned stub — it skews nextMilestoneId and
+    // was likely created by ensurePreconditions or showHeadlessMilestoneCreation
+    // for a phantom forward-reference. Surface as a fixable warning.
+    try {
+        const milestoneIds = findMilestoneIds(basePath);
+        const hasDbFile = existsSync(join(root, "gsd.db"));
+        for (const mid of milestoneIds) {
+            const isOrphan = isReusableGhostMilestone(basePath, mid)
+                || (!hasDbFile && isGhostMilestone(basePath, mid));
+            if (isOrphan) {
+                issues.push({
+                    severity: "warning",
+                    code: "orphan_milestone_dir",
+                    scope: "milestone",
+                    unitId: mid,
+                    message: `Orphan milestone directory: ${mid} — directory exists on disk with no DB row, no worktree, and no content files. This stub skews milestone ID generation and should be removed.`,
+                    file: `.gsd/milestones/${mid}`,
+                    fixable: true,
+                });
+                if (shouldFix("orphan_milestone_dir")) {
+                    try {
+                        const orphanPath = join(milestonesDir(basePath), mid);
+                        rmSync(orphanPath, { recursive: true, force: true });
+                        fixesApplied.push(`removed orphan milestone directory: ${mid}`);
+                    }
+                    catch {
+                        // Non-fatal — leave for manual cleanup
+                    }
+                }
+            }
+        }
+    }
+    catch {
+        // Non-fatal — orphan milestone directory check failed
+    }
 }
 /**
  * Build STATE.md markdown content from derived state.

package/dist/resources/extensions/gsd/error-classifier.js

@@ -34,7 +34,7 @@ const NETWORK_RE = /network|ECONNRESET|ETIMEDOUT|ECONNREFUSED|socket hang up|fet
 // Context overflow errors (context window/length exceeded) should be treated as server-class
 // transient errors so auto-mode can retry with reduced budget or fall back to a larger-context model.
 // See: https://github.com/gsd-build/gsd-2/issues/4528
-const SERVER_RE = /internal server error|500|502|503|overloaded|server_error|api_error|service.?unavailable|context (?:window|length) exceed|context window exceed/i;
+const SERVER_RE = /internal(?: server)?[ _-]?error|500|502|503|overloaded|server_error|api_error|service.?unavailable|context (?:window|length) exceed|context window exceed/i;
 // ECONNRESET/ECONNREFUSED are in NETWORK_RE (same-model retry first).
 const CONNECTION_RE = /terminated|connection.?(?:refused|error)|other side closed|EPIPE|network.?(?:is\s+)?unavailable|stream_exhausted(?:_without_result)?/i;
 // Catch-all for V8 JSON.parse errors: all modern variants end with "in JSON at position \d+".

package/dist/resources/extensions/gsd/forensics.js

@@ -10,7 +10,7 @@
 import { existsSync, mkdirSync, readFileSync, readdirSync, statSync, writeFileSync } from "node:fs";
 import { join, dirname, relative } from "node:path";
 import { fileURLToPath } from "node:url";
-import { homedir } from "node:os";
+import { getHomeDir } from "./home-dir.js";
 import { extractTrace } from "./session-forensics.js";
 import { nativeParseJsonlTail } from "./native-parser-bridge.js";
 import { MAX_JSONL_BYTES, parseJSONL } from "./jsonl-utils.js";
@@ -135,7 +135,7 @@ export async function handleForensics(args, ctx, pi) {
     // when import.meta.url resolves to the npm-global install path (Windows).
     let gsdSourceDir = dirname(fileURLToPath(import.meta.url));
     if (!existsSync(join(gsdSourceDir, "prompts"))) {
-        const gsdHome = process.env.GSD_HOME || join(homedir(), ".gsd");
+        const gsdHome = process.env.GSD_HOME || join(getHomeDir(), ".gsd");
         const fallback = join(gsdHome, "agent", "extensions", "gsd");
         if (existsSync(join(fallback, "prompts")))
             gsdSourceDir = fallback;
@@ -649,7 +649,7 @@ function detectMissingArtifacts(completedKeys, basePath, activeMilestone, anomal
  * the forensics memory-bloat guard in forensics-journal.test.ts — per-event
  * detail stays in the journal itself where the LLM can query it on demand.
  */
-function detectWorktreeOrphans(summary, anomalies) {
+export function detectWorktreeOrphans(summary, anomalies) {
     // 1. Orphan aggregate — severity depends on reason. In-progress orphans are
     // the #4761 consumer-side signal (live work sitting on an unmerged branch).
     for (const [reason, count] of Object.entries(summary.orphansByReason)) {
@@ -663,7 +663,7 @@ function detectWorktreeOrphans(summary, anomalies) {
             details: reason === "in-progress-unmerged"
                 ? "Auto-mode exited without completing a milestone; live work sits on an unmerged milestone branch. Run `/gsd auto` to resume, or merge manually."
                 : reason === "complete-unmerged"
-                    ? "A completed milestone's branch was never merged back to main. Run `/gsd health --fix` to resolve."
+                    ? "A completed milestone's branch was never merged back to main. Run `/gsd doctor fix` to resolve."
                     : `Reason: ${reason}.`,
         });
     }
@@ -1109,11 +1109,13 @@ function formatReportForPrompt(report) {
 // ─── Redaction ────────────────────────────────────────────────────────────────
 function redactForGitHub(text, basePath) {
     let result = text;
+    // Build regex that matches both / and \ separator variants (Windows)
+    // Normalize to / first, escape for regex, then replace each / with [/\\]
+    const esc = (s) => s.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
+    const pathRe = (p) => new RegExp(esc(p.replace(/\\/g, "/")).replace(/\//g, "[/\\\\]"), "gi");
     // Replace absolute paths
-    result = result.replaceAll(basePath, ".");
-    const home = process.env.HOME ?? process.env.USERPROFILE ?? "";
-    if (home)
-        result = result.replaceAll(home, "~");
+    result = result.replace(pathRe(basePath), ".");
+    result = result.replace(pathRe(getHomeDir()), "~");
     // Strip API key patterns
     result = result.replace(/sk-[a-zA-Z0-9]{20,}/g, "sk-***");
     result = result.replace(/Bearer\s+\S+/g, "Bearer ***");

package/dist/resources/extensions/gsd/git-service.js

@@ -18,6 +18,7 @@ import { SLICE_BRANCH_RE, QUICK_BRANCH_RE, WORKFLOW_BRANCH_RE } from "./branch-p
 import { nativeGetCurrentBranch, nativeDetectMainBranch, nativeBranchExists, nativeHasChanges, nativeAddAllWithExclusions, nativeHasStagedChanges, nativeCommit, nativeRmCached, nativeUpdateRef, nativeResetSoft, nativeCommitSubject, _resetHasChangesCache, } from "./native-git-bridge.js";
 import { GSDError, GSD_MERGE_CONFLICT, GSD_GIT_ERROR } from "./errors.js";
 import { getErrorMessage } from "./error-utils.js";
+import { isInfrastructureError } from "./auto/infra-errors.js";
 export const VALID_BRANCH_NAME = /^[a-zA-Z0-9_\-\/.]+$/;
 /**
  * Build a meaningful conventional commit message from task execution context.
@@ -775,6 +776,16 @@ function buildTurnSnapshotLabel(unitType, unitId) {
         .replace(/-{2,}/g, "-")
         .replace(/^[-/]+|[-/]+$/g, "") || "turn";
 }
+export function handleTurnGitActionError(action, err) {
+    if (isInfrastructureError(err)) {
+        throw err;
+    }
+    return {
+        action,
+        status: "failed",
+        error: getErrorMessage(err),
+    };
+}
 export function runTurnGitAction(args) {
     try {
         // Force fresh working-tree status per turn; nativeHasChanges caches briefly.
@@ -806,11 +817,7 @@ export function runTurnGitAction(args) {
         };
     }
     catch (err) {
-        return {
-            action: args.action,
-            status: "failed",
-            error: getErrorMessage(err),
-        };
+        return handleTurnGitActionError(args.action, err);
     }
 }
 // ─── Commit Type Inference ─────────────────────────────────────────────────

package/dist/resources/extensions/gsd/gsd-db.js

@@ -1321,6 +1321,15 @@ export function checkpointDatabase() {
     }
 }
 let _txDepth = 0;
+/**
+ * Whether the current call is running inside an active SQLite transaction.
+ * Statement-time recovery paths (e.g. VACUUM retry on a malformed memory
+ * store) MUST gate on this — SQLite refuses VACUUM inside a transaction
+ * and would mask the original error with a secondary "cannot VACUUM" throw.
+ */
+export function isInTransaction() {
+    return _txDepth > 0;
+}
 export function transaction(fn) {
     if (!currentDb)
         throw new GSDError(GSD_STALE_STATE, "gsd-db: No database open");
@@ -1335,8 +1344,8 @@ export function transaction(fn) {
             _txDepth--;
         }
     }
-    _txDepth++;
     currentDb.exec("BEGIN");
+    _txDepth++;
     try {
         const result = fn();
         currentDb.exec("COMMIT");
@@ -1369,8 +1378,8 @@ export function readTransaction(fn) {
             _txDepth--;
         }
     }
-    _txDepth++;
     currentDb.exec("BEGIN DEFERRED");
+    _txDepth++;
     try {
         const result = fn();
         currentDb.exec("COMMIT");