gsd-pi 2.78.0-dev.aeeb2ca00 → 2.78.1-dev.84a383f51

package/dist/resources/extensions/gsd/bootstrap/write-gate.js

@@ -441,8 +441,31 @@ export function shouldBlockQueueExecutionInSnapshot(snapshot, toolName, input, q
     };
 }
 // ─── Planning-unit tools-policy enforcement (#4934) ───────────────────────
+//
+// Runtime half of the declarative ToolsPolicy on UnitContextManifest. The
+// manifest assigns each unit type a tools mode; this predicate is what
+// actually rejects a tool call that violates it.
+//
+// Forensics: a discuss-milestone LLM turn used the host Edit tool to modify
+// index.html in test app b23 (~/Github/test-apps/b23). With this predicate
+// wired into the tool_call hook, the same call returns block=true with a
+// HARD BLOCK reason that the model cannot rationalize past.
+//
+// Activation: the hook supplies the policy resolved from the active unit's
+// manifest. When no unit is active (interactive sessions, unknown unit
+// types), the hook passes null and this predicate is a no-op — falling
+// through to the existing pendingGate / queue-execution / context-write
+// guards.
 const PLANNING_WRITE_TOOLS = new Set(["write", "edit", "multi_edit", "notebook_edit"]);
 const PLANNING_SUBAGENT_TOOLS = new Set(["subagent", "task"]);
+/**
+ * Read-only / planning-safe tools that any non-"all" mode allows. Mirrors
+ * QUEUE_SAFE_TOOLS / GATE_SAFE_TOOLS but is the inclusive default for
+ * planning units (which need their full discussion + research surface).
+ *
+ * gsd_* MCP tools are passed through unconditionally — they have their own
+ * domain validation (e.g. depth-verification gate, single-writer DB).
+ */
 const PLANNING_SAFE_TOOLS = new Set([
     "read", "grep", "find", "ls", "glob",
     "ask_user_questions",
@@ -458,6 +481,7 @@ function matchesAllowedGlob(absPath, basePath, globs) {
     const rel = relative(basePath, absPath);
     if (rel.startsWith("..") || isAbsolute(rel))
         return false;
+    // Normalize Windows separators for minimatch.
     const posix = rel.split(sep).join("/");
     return globs.some(g => minimatch(posix, g, { dot: false, nocase: false }));
 }
@@ -480,7 +504,12 @@ function blockReason(unitType, mode, what) {
  *   - "docs"       → like "planning" but also allows writes to paths
  *                    matching `allowedPathGlobs` relative to basePath.
  *
- * `policy` of null means "no manifest resolved" — pass-through.
+ * `pathOrCommand` is the file path for write/edit-shaped tools and the
+ * shell command for bash. Other tools ignore this argument.
+ *
+ * `policy` of null means "no manifest resolved" — pass-through. Callers
+ * that have no active unit (interactive sessions) pass null and this
+ * predicate is a no-op.
  */
 export function shouldBlockPlanningUnit(toolName, pathOrCommand, basePath, unitType, policy) {
     if (!policy)
@@ -488,6 +517,7 @@ export function shouldBlockPlanningUnit(toolName, pathOrCommand, basePath, unitT
     if (policy.mode === "all")
         return { block: false };
     const tool = toolName;
+    // Read-only mode: only Read-class tools are permitted.
     if (policy.mode === "read-only") {
         if (PLANNING_SAFE_TOOLS.has(tool))
             return { block: false };
@@ -496,9 +526,10 @@ export function shouldBlockPlanningUnit(toolName, pathOrCommand, basePath, unitT
         if (PLANNING_WRITE_TOOLS.has(tool) || tool === "bash" || PLANNING_SUBAGENT_TOOLS.has(tool)) {
             return { block: true, reason: blockReason(unitType, policy.mode, `${tool} is not permitted (read-only)`) };
         }
+        // Unknown tool in read-only mode — block by default.
         return { block: true, reason: blockReason(unitType, policy.mode, `tool "${tool}" is not on the read-only allowlist`) };
     }
-    // planning / docs modes
+    // planning / docs modes share the same surface for safe tools, bash, and subagent.
     if (PLANNING_SAFE_TOOLS.has(tool))
         return { block: false };
     if (tool.startsWith("gsd_"))
@@ -519,8 +550,10 @@ export function shouldBlockPlanningUnit(toolName, pathOrCommand, basePath, unitT
             return { block: true, reason: blockReason(unitType, policy.mode, `${tool} called with empty path`) };
         }
         const absPath = isAbsolute(pathOrCommand) ? pathOrCommand : resolve(basePath, pathOrCommand);
+        // Always allow .gsd/ writes — that's where planning artifacts live.
         if (isPathUnderGsd(absPath, basePath))
             return { block: false };
+        // docs mode additionally allows the manifest's allowedPathGlobs.
         if (policy.mode === "docs" && matchesAllowedGlob(absPath, basePath, policy.allowedPathGlobs)) {
             return { block: false };
         }
@@ -529,5 +562,8 @@ export function shouldBlockPlanningUnit(toolName, pathOrCommand, basePath, unitT
             reason: blockReason(unitType, policy.mode, `cannot ${tool} "${pathOrCommand}" — writes are restricted to .gsd/${policy.mode === "docs" ? " and " + policy.allowedPathGlobs.join(", ") : ""}`),
         };
     }
+    // Unknown tool name — pass through. Other layers (queue, pending-gate,
+    // CONTEXT.md write) catch known mutating shapes; defaulting to allow here
+    // avoids breaking gsd_* MCP tools or future safe additions.
     return { block: false };
 }

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-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`.
@@ -193,6 +195,8 @@ 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-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

@@ -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}.`,
         });
     }

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");

package/dist/resources/extensions/gsd/guided-flow.js

@@ -33,7 +33,9 @@ import { showProjectInit, offerMigration } from "./init-wizard.js";
 import { validateDirectory } from "./validate-directory.js";
 import { showConfirm } from "../shared/tui.js";
 import { debugLog } from "./debug-logger.js";
-import { findMilestoneIds, nextMilestoneId, reserveMilestoneId, getReservedMilestoneIds, clearReservedMilestoneIds } from "./milestone-ids.js";
+import { findMilestoneIds, clearReservedMilestoneIds } from "./milestone-ids.js";
+import { nextMilestoneIdReserved } from "./milestone-id-reservation.js";
+export { nextMilestoneIdReserved } from "./milestone-id-reservation.js";
 import { parkMilestone, discardMilestone } from "./milestone-actions.js";
 import { selectAndApplyModel } from "./auto-model-selection.js";
 import { DISCUSS_TOOLS_ALLOWLIST } from "./constants.js";
@@ -43,18 +45,6 @@ import { runPreparation, formatCodebaseBrief, formatPriorContextBrief, } from ".
 export { MILESTONE_ID_RE, generateMilestoneSuffix, nextMilestoneId, extractMilestoneSeq, parseMilestoneId, milestoneIdSort, maxMilestoneNum, findMilestoneIds, reserveMilestoneId, claimReservedId, getReservedMilestoneIds, clearReservedMilestoneIds, } from "./milestone-ids.js";
 export { showQueue, handleQueueReorder, showQueueAdd, buildExistingMilestonesContext, } from "./guided-flow-queue.js";
 import { logWarning } from "./workflow-logger.js";
-// ─── ID Generation with Reservation ─────────────────────────────────────────
-/**
- * Generate the next milestone ID, accounting for reserved IDs, and reserve it.
- * Ensures any preview ID shown in the UI matches what `gsd_milestone_generate_id`
- * will later return.
- */
-function nextMilestoneIdReserved(existingIds, uniqueEnabled) {
-    const allIds = [...new Set([...existingIds, ...getReservedMilestoneIds()])];
-    const id = nextMilestoneId(allIds, uniqueEnabled);
-    reserveMilestoneId(id);
-    return id;
-}
 function needsPlanV2Gate(state) {
     return state.phase === "executing"
         || state.phase === "summarizing"
@@ -675,13 +665,17 @@ export async function showHeadlessMilestoneCreation(ctx, pi, basePath, seedConte
     clearReservedMilestoneIds();
     // Ensure .gsd/ is bootstrapped
     bootstrapGsdProject(basePath);
+    const { ensureDbOpen } = await import("./bootstrap/dynamic-tools.js");
+    await ensureDbOpen(basePath);
     // Generate next milestone ID
     const existingIds = findMilestoneIds(basePath);
     const prefs = loadEffectiveGSDPreferences();
-    const nextId = nextMilestoneIdReserved(existingIds, prefs?.preferences?.unique_milestone_ids ?? false);
-    // Create milestone directory
-    const milestoneDir = join(gsdRoot(basePath), "milestones", nextId, "slices");
-    mkdirSync(milestoneDir, { recursive: true });
+    const nextId = nextMilestoneIdReserved(existingIds, prefs?.preferences?.unique_milestone_ids ?? false, basePath);
+    // Fix #4996: Do NOT pre-create the milestone directory here.
+    // atomicWriteAsync (used by all artifact writers) calls mkdir lazily before
+    // each write, so every path through saveArtifactToDb / saveFile is already
+    // lazy-mkdir-safe. Pre-creating the dir before the discuss flow runs leaves
+    // an orphan stub if discuss is abandoned — that stub later skews nextMilestoneId.
     // Build and dispatch the headless discuss prompt
     const prompt = buildHeadlessDiscussPrompt(nextId, seedContext, basePath);
     // Set pending auto start (auto-mode triggers on "Milestone X ready." via checkAutoStartAfterDiscuss)
@@ -865,9 +859,11 @@ export async function showDiscuss(ctx, pi, basePath) {
             }), "gsd-discuss", ctx, "discuss-milestone");
         }
         else if (choice === "skip_milestone") {
+            const { ensureDbOpen } = await import("./bootstrap/dynamic-tools.js");
+            await ensureDbOpen(basePath);
             const milestoneIds = findMilestoneIds(basePath);
             const uniqueMilestoneIds = !!loadEffectiveGSDPreferences()?.preferences?.unique_milestone_ids;
-            const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds);
+            const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds, basePath);
             pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: nextId, step: false, createdAt: Date.now() });
             await dispatchWorkflow(pi, await prepareAndBuildDiscussPrompt(ctx, pi, nextId, `New milestone ${nextId}.`, basePath), "gsd-run", ctx, "discuss-milestone");
         }
@@ -1223,7 +1219,7 @@ async function handleMilestoneActions(ctx, pi, basePath, milestoneId, milestoneT
     if (choice === "skip") {
         const milestoneIds = findMilestoneIds(basePath);
         const uniqueMilestoneIds = !!loadEffectiveGSDPreferences()?.preferences?.unique_milestone_ids;
-        const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds);
+        const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds, basePath);
         pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: nextId, step: stepMode, createdAt: Date.now() });
         await dispatchWorkflow(pi, await prepareAndBuildDiscussPrompt(ctx, pi, nextId, `New milestone ${nextId}.`, basePath), "gsd-run", ctx, "discuss-milestone");
         return true;
@@ -1291,6 +1287,10 @@ export async function showSmartEntry(ctx, pi, basePath, options) {
     // ── Ensure .gitignore has baseline patterns ──────────────────────────
     ensureGitignore(basePath);
     untrackRuntimeFiles(basePath);
+    {
+        const { ensureDbOpen } = await import("./bootstrap/dynamic-tools.js");
+        await ensureDbOpen(basePath);
+    }
     // ── Self-heal stale runtime records from crashed auto-mode sessions ──
     selfHealRuntimeRecords(basePath, ctx);
     const interrupted = await assessInterruptedSession(basePath);
@@ -1388,7 +1388,7 @@ export async function showSmartEntry(ctx, pi, basePath, options) {
             }
         }
         const uniqueMilestoneIds = !!loadEffectiveGSDPreferences()?.preferences?.unique_milestone_ids;
-        const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds);
+        const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds, basePath);
         const isFirst = milestoneIds.length === 0;
         if (isFirst) {
             // First ever — skip wizard, just ask directly
@@ -1446,7 +1446,7 @@ export async function showSmartEntry(ctx, pi, basePath, options) {
         if (choice === "new_milestone") {
             const milestoneIds = findMilestoneIds(basePath);
             const uniqueMilestoneIds = !!loadEffectiveGSDPreferences()?.preferences?.unique_milestone_ids;
-            const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds);
+            const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds, basePath);
             pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: nextId, step: stepMode, createdAt: Date.now() });
             await dispatchWorkflow(pi, await prepareAndBuildDiscussPrompt(ctx, pi, nextId, `New milestone ${nextId}.`, basePath), "gsd-run", ctx, "discuss-milestone");
         }
@@ -1510,7 +1510,7 @@ export async function showSmartEntry(ctx, pi, basePath, options) {
         else if (choice === "skip_milestone") {
             const milestoneIds = findMilestoneIds(basePath);
             const uniqueMilestoneIds = !!loadEffectiveGSDPreferences()?.preferences?.unique_milestone_ids;
-            const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds);
+            const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds, basePath);
             pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: nextId, step: stepMode, createdAt: Date.now() });
             await dispatchWorkflow(pi, await prepareAndBuildDiscussPrompt(ctx, pi, nextId, `New milestone ${nextId}.`, basePath), "gsd-run", ctx, "discuss-milestone");
         }
@@ -1600,7 +1600,7 @@ export async function showSmartEntry(ctx, pi, basePath, options) {
             else if (choice === "skip_milestone") {
                 const milestoneIds = findMilestoneIds(basePath);
                 const uniqueMilestoneIds = !!loadEffectiveGSDPreferences()?.preferences?.unique_milestone_ids;
-                const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds);
+                const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds, basePath);
                 pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: nextId, step: stepMode, createdAt: Date.now() });
                 await dispatchWorkflow(pi, await prepareAndBuildDiscussPrompt(ctx, pi, nextId, `New milestone ${nextId}.`, basePath), "gsd-run", ctx, "discuss-milestone");
             }