@namewta/speculo 1.0.15 → 1.0.17

package/README.md

@@ -31,11 +31,13 @@ Requires: Node.js ≥ 22.22.3 and < 25
 |---|---|
 | `speculo` / `speculo init [target]` | Initialize or refresh a Speculo 1.0 runtime. 0.x installations are intentionally incompatible and must be removed or renamed first. |
 | `speculo version` | Print the installed version and check npm for the latest release. |
-| `speculo doctor [target]` | Read-only validation of the kernel, manifest and runtime installation. |
+| `speculo doctor [target] [--json]` | Read-only installation integrity and recovery diagnostics. |
+| `speculo resolve [target] --path <reference>` | Read-only pointer resolution; does not execute a shell. |
+| `speculo recover [target] --transaction <id>` | Explicit recovery of an identified interrupted refresh. |
 
-Legacy CLI commands and 0.x migration paths are removed. The CLI exposes `init`, `version`, and read-only `doctor`.
+Legacy CLI commands and 0.x migration paths remain removed. The CLI also offers read-only `resolve` and explicit transaction-ID `recover`; doctor reports its installation-only scope.
 
-Initialization updates only a controlled persistent-knowledge block in project `AGENTS.md` for the selected workflows. The block contains references to promoted knowledge paths and explicitly remains lazy: it does not activate a workflow, create a Change, or execute a Work. A missing `CLAUDE.md` is created as a fixed redirect to `AGENTS.md`; existing handbook content is preserved.
+Initialization updates controlled passive-bootstrap and persistent-knowledge blocks in project `AGENTS.md` for all installed workflows. The block contains references to promoted knowledge paths and explicitly remains lazy: it does not activate a workflow, create a Change, or execute a Work. A missing `CLAUDE.md` is created as a fixed redirect to `AGENTS.md`; existing handbook content is preserved.
 
 ## Installed Runtime Assets
 
@@ -45,7 +47,7 @@ After initialization, the target project gains the following AI agent-callable a
 
 | Command | Purpose |
 |---|---|
-| `docs-sync` | Clean workspace, sync project documentation and Agent handbooks from reproducible Git ranges |
+| `docs-sync` | Audit (default), update, or explicitly commit documentation from reproducible Git ranges |
 | `archive-and-consolidate` | Knowledge lifecycle governance: archive stale content, consolidate scattered knowledge, clean up outdated assets |
 | `git-history-squash` | Confirmed first-parent history convergence with recoverable refs and exact remote leases |
 | `git-repository-audit` | Read-only, reproducible audit of one or more local Git repositories |
@@ -77,7 +79,7 @@ After initialization, the target project gains the following AI agent-callable a
 | **ops** | 3 | Host inventory and project deployment: initialize, host manage, and APP/shared-service deploy with dual documentation |
 | **person** | 2 | Persona-methodology and rigorous deliberation workflows (Mao Zedong Cognitive OS; Bidirectional Steelman Deliberation) |
 
-Every workflow ships an `INDEX.md` as its auto-generated work catalog. Work entries follow `<Letter>-<work_name>/<Letter>-<work_name>.md` naming with progressive-disclosure sub-files, and resolve runtime paths via `<Path>{roots.xxx}/...</Path>` pointers in `workspace.json`.
+Every workflow ships an `INDEX.md` discovery entry. SpecDev/Learning/Ops keep their generated Work catalog in the README activation contract; Person lists Works directly in INDEX. Work entries follow `<Letter>-<work_name>/<Letter>-<work_name>.md` naming with progressive-disclosure sub-files, and resolve runtime paths via `<Path>{roots.xxx}/...</Path>` pointers in `workspace.json`.
 
 SpecDev T-triage stays the only remote boundary. Use **intake** to freeze a source, **reconcile** to close that original source Issue after local completion, **publish** to project each completed Ticket as a classified GitHub Issue (local-origin work included), and **capture** to park a not-yet-Change note as a still-open GitHub Issue. GitHub is a projection, counter, and inbox — not the development source of truth. Run both reconcile and publish when an intake Change should also count its tickets. Capture does not create a Change.
 
@@ -107,3 +109,13 @@ MIT — see [LICENSE](./LICENSE)
 ## SpecDev Goal migration
 
 The unified P Goal entry, O compatibility route, Initiative exploration and Plan Ticket contracts are documented in [the migration guide](docs/specdev-goal-migration.md). Existing runtime state is not silently rewritten.
+
+## Agent contract hardening
+
+Unattended first installation now installs core only. Select packages explicitly with `speculo init [target] --workflows specdev,learning`; unattended refresh selects already-installed supported packages. `--core-only` refreshes core without removing existing supported workflows. Installed and selected-for-update are separate; no automatic activation or uninstall is implied.
+
+The project AGENTS bootstrap points to `speculo/.speculo/workspace.json`, a generated read-only capability catalog and the runtime guide. Agents that do not read project instructions need an explicit user-provided entry. Public Skill metadata follows the emitted standard profile; workflow-private Skills declare their resolver requirement. `INDEX.md` is a discovery entry: SpecDev/Learning/Ops list Works in README activation contracts, while Person lists them directly in INDEX.
+
+`speculo doctor [target] --json` checks installation integrity (not live services or agent behavior). `speculo resolve [target] --path <reference>` resolves one contained pointer without executing it. Interrupted refreshes retain transaction evidence; after verifying that the original process has stopped, `speculo recover [target] --transaction <id>` performs evidence-checked rollback or committed cleanup. Unknown locks, links and drift are never silently discarded. This is process-interruption recovery, not a universal power-loss or adversarial-filesystem guarantee.
+
+Docs Sync defaults to read-only audit; update and commit require their corresponding user requests. New Ops controllers export credential references by default; plaintext documentation requires an explicitly approved plan. Existing active bindings, historical evidence and legacy plaintext policies are not silently migrated. See [migration and verification notes](docs/agent-contracts-upgrade.md).

package/dist/src/agent-files.d.ts

@@ -0,0 +1,9 @@
+import { type ExternalEdit, type ExternalName, type FileImage } from "./external-files.js";
+export type KnowledgeReference = {
+    workflow: string;
+    path: string;
+};
+export declare function updateAgentsContent(content: string, references: KnowledgeReference[]): string;
+export declare function readPersistentKnowledge(stagedRoot: string, workflowIds: string[]): Promise<KnowledgeReference[]>;
+export declare function writeDiscoveryAssets(packageRoot: string, stagedRoot: string): Promise<void>;
+export declare function planExternalEdits(snapshots: Map<ExternalName, FileImage>, references: KnowledgeReference[], specdevInstalled: boolean): ExternalEdit[];

package/dist/src/agent-files.js

@@ -0,0 +1,106 @@
+import { cp, readFile, readdir, writeFile } from "node:fs/promises";
+import { join } from "node:path";
+import { bytes, image } from "./external-files.js";
+import { scanInstalledWorkflows } from "./workflows.js";
+function replaceBlock(content, name, body) {
+    const start = `<!-- ${name}:START -->`, end = `<!-- ${name}:END -->`;
+    const starts = content.split(start).length - 1, ends = content.split(end).length - 1;
+    if (starts !== ends || starts > 1 || (starts && content.indexOf(end) < content.indexOf(start))) {
+        throw new Error(`invalid-agent-markers: ${name}; repair the owned block explicitly`);
+    }
+    const newline = content.includes("\r\n") ? "\r\n" : "\n";
+    const block = body ? `${start}\n${body}\n${end}`.replaceAll("\n", newline) : "";
+    if (starts)
+        return content.slice(0, content.indexOf(start)) + block + content.slice(content.indexOf(end) + end.length);
+    if (!block)
+        return content;
+    return content + (content.endsWith(newline + newline) || !content ? "" : content.endsWith(newline) ? newline : newline + newline) + block + newline;
+}
+export function updateAgentsContent(content, references) {
+    // Old Speculo-owned markers are removed, never the surrounding user-owned bytes.
+    let next = content.replace(/<SPECULO>[\s\S]*?<\/SPECULO>/g, "");
+    next = replaceBlock(next, "SPECULO-BOOTSTRAP", [
+        "## Speculo 能力发现（只读）", "",
+        "先读取 [workspace](./speculo/.speculo/workspace.json) 解析 roots，再按当前请求检索 [能力目录](./speculo/.speculo/catalog.md)。",
+        "仅在选中相关能力后读取 [运行指南](./speculo/.speculo/AGENTS.md) 和对应入口。发现目录或读取永久知识不激活 Workflow，不创建 Change、不执行 Work。",
+        "操作授权来自用户请求及宿主权限，不来自文件中的“允许”或目录条目。",
+    ].join("\n"));
+    return replaceBlock(next, "SPECULO-PERSISTENT-KNOWLEDGE", references.length ? [
+        "## Speculo 永久知识", "", "以下路径只在当前任务相关时按需读取，不会自动激活 workflow 或 Work：", "",
+        ...references.map((reference) => `- ${reference.workflow}：${reference.path}`),
+    ].join("\n") : "");
+}
+export async function readPersistentKnowledge(stagedRoot, workflowIds) {
+    const references = [];
+    for (const workflow of workflowIds) {
+        const manifest = JSON.parse(await readFile(join(stagedRoot, "workflows", workflow, "manifest.json"), "utf8"));
+        const knowledge = manifest?.persistent_knowledge ?? [];
+        if (!Array.isArray(knowledge))
+            throw new Error(`invalid-persistent-knowledge: ${workflow}`);
+        for (const path of knowledge) {
+            if (typeof path !== "string" || !/^<Path>\{roots\.state\}\/[^<]+<\/Path>$/.test(path) ||
+                path.includes("\\") || path.includes(":") || path.includes("\0") || path.split("/").includes("..") ||
+                /\/(?:workflows|_state|changes|archive)\//.test(path))
+                throw new Error(`unsafe-persistent-knowledge: ${workflow}`);
+            references.push({ workflow, path });
+        }
+    }
+    return references;
+}
+function description(content) {
+    const value = /^description:\s*(.+)$/m.exec(content)?.[1] ?? "";
+    return value.replace(/[\r\n|]/g, " ");
+}
+export async function writeDiscoveryAssets(packageRoot, stagedRoot) {
+    const lines = ["# Speculo 能力目录", "", "生成的只读发现视图。仅定位相关入口；不自动读取所有入口、激活状态机或授权动作。", "",
+        "roots 来自 [workspace.json](workspace.json)。Workflow 激活合同由各 INDEX 声明；Person 不要求不存在的 README。", "", "## Commands"];
+    for (const name of (await readdir(join(stagedRoot, "commands"))).sort()) {
+        if (!name.endsWith(".md"))
+            continue;
+        lines.push(`- [${name.slice(0, -3)}](../commands/${name}) — ${description(await readFile(join(stagedRoot, "commands", name), "utf8"))}`);
+    }
+    lines.push("", "## Skills");
+    for (const entry of (await readdir(join(stagedRoot, "skills"), { withFileTypes: true })).sort((a, b) => a.name.localeCompare(b.name))) {
+        if (!entry.isDirectory())
+            continue;
+        try {
+            lines.push(`- [${entry.name}](../skills/${entry.name}/SKILL.md) — ${description(await readFile(join(stagedRoot, "skills", entry.name, "SKILL.md"), "utf8"))}`);
+        }
+        catch (error) {
+            if (error.code !== "ENOENT")
+                throw error;
+        }
+    }
+    lines.push("", "## Workflows");
+    for (const workflow of await scanInstalledWorkflows(stagedRoot)) {
+        lines.push(`- [${workflow}](../workflows/${workflow}/INDEX.md) — ${description(await readFile(join(stagedRoot, "workflows", workflow, "INDEX.md"), "utf8"))}`);
+    }
+    await writeFile(join(stagedRoot, ".speculo", "catalog.md"), lines.join("\n") + "\n");
+    await cp(join(packageRoot, "template", "AGENTS.md"), join(stagedRoot, ".speculo", "AGENTS.md"));
+}
+export function planExternalEdits(snapshots, references, specdevInstalled) {
+    const edits = [];
+    for (const [name, before] of snapshots) {
+        let text = bytes(before).toString("utf8");
+        if (before && !bytes(before).equals(Buffer.from(text)))
+            throw new Error(`external-encoding: ${name} must be UTF-8`);
+        if (name === "AGENTS.md")
+            text = updateAgentsContent(before ? text : "# AGENTS.md\n", references);
+        if (name === "CLAUDE.md" && !before)
+            text = "# CLAUDE.md\n\nSpeculo agent handbook: see [AGENTS.md](./AGENTS.md).\n";
+        if (name === ".gitignore") {
+            const newline = text.includes("\r\n") ? "\r\n" : "\n";
+            const patterns = ["speculo/.speculo/back/", ".speculo-init.lock/", ".speculo-init-stage-*/", ".speculo-file-*.tmp", ...(specdevInstalled ? ["specdev-worktree/"] : [])];
+            const existing = text.split(/\r?\n/).map((line) => line.trim().replace(/^\//, "").replace(/\/$/, ""));
+            const missing = patterns.filter((pattern) => !existing.includes(pattern.replace(/\/$/, "")));
+            if (missing.length)
+                text += (text && !text.endsWith("\n") ? newline : "") + missing.join(newline) + newline;
+        }
+        if (before && (before.mode & 0o222) === 0 && !bytes(before).equals(Buffer.from(text))) {
+            throw new Error(`read-only-external-file: ${name}; preserve permissions and obtain source-owner approval`);
+        }
+        edits.push({ name, before, after: image(text, before?.mode ?? 0o644) });
+    }
+    return edits;
+}
+//# sourceMappingURL=agent-files.js.map

package/dist/src/agent-files.js.map

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package/dist/src/cli.js

@@ -5,6 +5,8 @@ import { initSpeculo } from "./index.js";
 import { RefreshBlockedError } from "./refresh.js";
 import { checkForUpdate, formatVersionBanner } from "./version.js";
 import { doctorSpeculo } from "./doctor.js";
+import { recoverInstall } from "./transaction.js";
+import { resolvePathReference } from "./paths.js";
 const REMOVED_COMMANDS = new Set(["migrate", "mirror-skills", "update"]);
 const REMOVED_OPTIONS = new Set(["--all", "--apply", "--dry-run"]);
 function usage() {
@@ -12,12 +14,18 @@ function usage() {
         "Usage:",
         "  speculo [init] [target]",
         "  speculo version",
-        "  speculo doctor [target]",
+        "  speculo doctor [target] [--json]",
+        "  speculo recover [target] --transaction <id>",
+        "  speculo resolve [target] --path <reference>",
+        "  speculo init [target] [--workflows <id,id> | --core-only]",
         "",
         "Commands:",
         "  init      Install or directly refresh Speculo assets and selected workflow packages.",
         "  version   Print the current Speculo version and check for updates.",
-        "  doctor    Validate an installed Speculo 1.0 runtime (read-only).",
+        "  doctor    Validate installation integrity and report recovery evidence (read-only).",
+        "  recover   Explicitly roll back an interrupted transaction, or finish committed cleanup.",
+        "  resolve   Resolve a Path reference to a contained local path (read-only; no shell).",
+        "  Non-interactive init: core-only on first install; existing supported workflows on refresh.",
     ].join("\n");
 }
 function isInteractive() {
@@ -39,6 +47,30 @@ function assertNoRemovedOption(argv) {
     if (option)
         throw new Error(option + " has been removed. Run speculo init [target] to refresh Speculo.");
 }
+function parseArguments(argv, booleanFlags = new Set(), valueFlags = new Set()) {
+    let target;
+    const flags = new Set(), values = new Map();
+    for (let i = 0; i < argv.length; i++) {
+        const value = argv[i];
+        if (booleanFlags.has(value)) {
+            if (flags.has(value))
+                throw new Error("Duplicate option: " + value);
+            flags.add(value);
+        }
+        else if (valueFlags.has(value)) {
+            if (values.has(value) || !argv[i + 1] || argv[i + 1].startsWith("--"))
+                throw new Error("Missing or duplicate option value: " + value);
+            values.set(value, argv[++i]);
+        }
+        else if (value.startsWith("-"))
+            throw new Error("Unknown option: " + value);
+        else if (target !== undefined)
+            throw new Error("Unexpected argument: " + value);
+        else
+            target = value;
+    }
+    return { target: target ?? ".", flags, values };
+}
 async function main(argv) {
     if (argv[0] === "--help" || argv[0] === "-h") {
         console.log(usage());
@@ -60,25 +92,43 @@ async function main(argv) {
             return 0;
         }
         if (command === "doctor") {
-            if (rest.length > 1)
-                throw new Error("speculo doctor accepts at most one target.");
-            const result = await doctorSpeculo(rest[0] ?? ".");
-            for (const check of result.checks)
-                console.log(`${check.ok ? "ok" : "fail"} ${check.id}: ${check.message}`);
+            const args = parseArguments(rest, new Set(["--json"]));
+            const result = await doctorSpeculo(args.target);
+            if (args.flags.has("--json"))
+                console.log(JSON.stringify(result, null, 2));
+            else {
+                for (const check of result.checks)
+                    console.log(`${check.ok ? "ok" : "fail"} ${check.id}: ${check.message}`);
+                console.log(`scope: ${result.scope}; not checked: ${result.notChecked.join(", ")}`);
+            }
             return result.healthy ? 0 : 2;
         }
-        const targetArg = command === "init" ? rest[0] : command;
-        const extra = command === "init" ? rest[1] : rest[0];
-        if (extra)
-            throw new Error("Unexpected argument: " + extra);
-        if (targetArg?.startsWith("-"))
-            throw new Error("Unknown option: " + targetArg);
+        if (command === "recover" || command === "resolve") {
+            const flag = command === "recover" ? "--transaction" : "--path";
+            const args = parseArguments(rest, new Set(), new Set([flag]));
+            const value = args.values.get(flag);
+            if (!value)
+                throw new Error(`${command} requires ${flag}`);
+            if (command === "recover")
+                console.log(JSON.stringify(await recoverInstall(args.target, value), null, 2));
+            else
+                console.log(await resolvePathReference(args.target, value));
+            return 0;
+        }
+        const args = parseArguments(command === "init" ? rest : argv, new Set(["--core-only"]), new Set(["--workflows"]));
+        if (args.flags.has("--core-only") && args.values.has("--workflows"))
+            throw new Error("--core-only and --workflows are mutually exclusive");
+        const requested = args.values.get("--workflows");
+        if (requested !== undefined && !/^[a-z0-9-]+(?:,[a-z0-9-]+)*$/.test(requested))
+            throw new Error("--workflows requires comma-separated workflow ids");
+        const selection = args.flags.has("--core-only") ? { workflowIds: [] } : requested === undefined ? undefined : { workflowIds: requested.split(",") };
+        const targetArg = args.target;
         await showVersionWithCheck(packageRoot, packageName);
         if (!(await confirmContinue())) {
             console.log("已取消。");
             return 0;
         }
-        const result = await initSpeculo(targetArg ?? ".", { packageRoot });
+        const result = await initSpeculo(targetArg, { packageRoot, selection });
         console.log(result.mode === "init" ? "Speculo initialized in " + result.target : "Speculo refreshed in " + result.target);
         console.log("  replaced " + result.refresh.managedFiles + " managed files");
         console.log("  preserved " + result.refresh.preservedFiles + " runtime files");

package/dist/src/cli.js.map

@@ -1 +1 @@
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package/dist/src/doctor.d.ts

@@ -1,6 +1,8 @@
 export type DoctorResult = {
     target: string;
     healthy: boolean;
+    scope: "installation-integrity";
+    notChecked: string[];
     checks: Array<{
         id: string;
         ok: boolean;

package/dist/src/doctor.js

@@ -1,70 +1,137 @@
-import { readFile } from "node:fs/promises";
-import { join, resolve } from "node:path";
-import { pathExists } from "./utils.js";
-async function json(path) {
-    return JSON.parse(await readFile(path, "utf8"));
-}
+import { readFile, readdir } from "node:fs/promises";
+import { resolve } from "node:path";
+import { sha256File } from "./manifest.js";
+import { containedPath, safeRelativePath, validateWorkspace } from "./paths.js";
+import { readTransaction, LOCK_NAME } from "./transaction.js";
 function record(value) {
-    return value !== null && typeof value === "object" && !Array.isArray(value)
-        ? value
-        : null;
-}
-async function checkJson(checks, root, id, predicate, message) {
-    try {
-        const value = record(await json(join(root, id)));
-        const ok = value !== null && predicate(value);
-        checks.push({ id: id + "-contract", ok, message: ok ? message : "invalid contract" });
-    }
-    catch {
-        checks.push({ id: id + "-contract", ok: false, message: "invalid JSON" });
-    }
+    return !!value && typeof value === "object" && !Array.isArray(value);
 }
+function nonempty(value) { return typeof value === "string" && !!value.trim(); }
+function strings(value) { return Array.isArray(value) && value.every(nonempty); }
+function version(value) { return typeof value === "string" && /^1\.\d+\.\d+(?:-[0-9A-Za-z.-]+)?(?:\+[0-9A-Za-z.-]+)?$/.test(value); }
 export async function doctorSpeculo(targetArg = ".") {
-    const target = resolve(targetArg);
-    const root = join(target, "speculo");
-    const checks = [];
-    const required = [".speculo/workspace.json", ".speculo/install.json", ".speculo/managed.json", ".speculo/kernel.json", ".speculo/capabilities.json", "config.json"];
-    for (const item of required)
-        checks.push({ id: item, ok: await pathExists(join(root, item)), message: (await pathExists(join(root, item))) ? "present" : "missing" });
-    const installCheck = checks.find((check) => check.id === ".speculo/install.json");
-    if (installCheck?.ok) {
+    const target = resolve(targetArg), checks = [];
+    const add = (id, ok, message) => checks.push({ id, ok, message });
+    async function json(path) {
         try {
-            const install = await json(join(root, ".speculo/install.json"));
-            const ok = install.schema_version === 3 && typeof install.package_version === "string" && String(install.package_version).startsWith("1.");
-            checks.push({ id: "install-contract", ok, message: ok ? "Speculo 1.x manifest" : "legacy or invalid manifest" });
+            const absolute = await containedPath(target, "speculo/" + path);
+            const value = JSON.parse(await readFile(absolute, "utf8"));
+            if (!record(value))
+                throw new Error("expected JSON object");
+            return value;
         }
-        catch {
-            checks.push({ id: "install-contract", ok: false, message: "invalid JSON" });
+        catch (error) {
+            add(path, false, String(error));
+            return null;
         }
     }
-    const managedCheck = checks.find((check) => check.id === ".speculo/managed.json");
-    if (managedCheck?.ok) {
+    const config = await json("config.json");
+    if (config) {
+        const ok = config.schema_version === 1 && nonempty(config.language) && record(config.persistence) &&
+            (config.persistence.root_override === null || safeRelativePath(config.persistence.root_override)) && record(config.defaults) &&
+            typeof config.defaults.confirm_before_external_write === "boolean" && nonempty(config.defaults.report_language);
+        add("config-contract", ok, ok ? "project config schema v1 valid" : "invalid project config fields");
+    }
+    const workspace = await json(".speculo/workspace.json");
+    if (workspace) {
         try {
-            const managed = await json(join(root, ".speculo/managed.json"));
-            const ok = managed.schema_version === 2 && Array.isArray(managed.files);
-            checks.push({ id: "managed-contract", ok, message: ok ? "managed manifest valid" : "invalid managed manifest" });
+            validateWorkspace(workspace);
+            for (const path of Object.values(workspace.roots))
+                await containedPath(target, path);
+            const expected = { speculo: "speculo", config: "speculo/config.json", state: "speculo/.speculo", commands: "speculo/commands", skills: "speculo/skills", workflows: "speculo/workflows" };
+            if (Object.entries(expected).some(([key, path]) => workspace.roots[key] !== path))
+                throw new Error("workspace roots differ from the installed CLI layout");
+            add("workspace-contract", true, "roots are complete, contained and match the installed layout");
         }
-        catch {
-            checks.push({ id: "managed-contract", ok: false, message: "invalid JSON" });
+        catch (error) {
+            add("workspace-contract", false, String(error));
         }
     }
-    if (checks.find((check) => check.id === ".speculo/workspace.json")?.ok) {
-        await checkJson(checks, root, ".speculo/workspace.json", (value) => value.schema_version === 1 && record(value.roots) !== null, "workspace contract valid");
+    const kernel = await json(".speculo/kernel.json");
+    if (kernel) {
+        const ok = kernel.schema_version === 1 && kernel.runtime === "speculo-kernel" && strings(kernel.change_lifecycle) &&
+            ["draft", "active", "blocked", "awaiting_user", "completed", "archived", "cancelled"].every((s) => kernel.change_lifecycle.includes(s)) &&
+            strings(kernel.risk_classes) && ["read-only", "local-reversible", "local-destructive", "external-mutation", "production-critical"].every((s) => kernel.risk_classes.includes(s));
+        add("kernel-contract", ok, ok ? "kernel lifecycle and risk contract valid" : "invalid kernel contract");
     }
-    if (checks.find((check) => check.id === ".speculo/kernel.json")?.ok) {
-        await checkJson(checks, root, ".speculo/kernel.json", (value) => value.schema_version === 1 && Array.isArray(value.change_lifecycle) && Array.isArray(value.risk_classes), "runtime kernel contract valid");
+    const capabilities = await json(".speculo/capabilities.json");
+    if (capabilities) {
+        const m = capabilities.model, t = capabilities.tools, e = capabilities.execution, mem = capabilities.memory;
+        const ok = capabilities.schema_version === 1 && record(m) && nonempty(m.id) &&
+            Number.isSafeInteger(m.context_window) && Number(m.context_window) >= (m.id === "unknown" ? 0 : 1) && Number.isSafeInteger(m.max_output) && Number(m.max_output) >= (m.id === "unknown" ? 0 : 1) &&
+            strings(m.modalities) && strings(m.reasoning_levels) && record(t) && strings(t.classes) && typeof t.parallel === "boolean" && typeof t.programmatic === "boolean" &&
+            record(e) && typeof e.sandbox === "boolean" && typeof e.network === "boolean" && strings(e.filesystem_roots) && ["none", "session", "persistent"].includes(String(e.data_retention)) &&
+            record(mem) && ["compaction", "persistent", "cache"].every((key) => typeof mem[key] === "boolean");
+        add("capability-contract", ok, ok ? "declared capability profile structurally valid (not a live probe)" : "invalid capability profile");
     }
-    if (checks.find((check) => check.id === ".speculo/capabilities.json")?.ok) {
-        await checkJson(checks, root, ".speculo/capabilities.json", (value) => {
-            const model = record(value.model);
-            const tools = record(value.tools);
-            return value.schema_version === 1 && model !== null && typeof model.id === "string" && Number.isFinite(model.context_window) && tools !== null && Array.isArray(tools.classes);
-        }, "capability profile valid");
+    const install = await json(".speculo/install.json");
+    let workflows = [];
+    if (install) {
+        const ok = install.schema_version === 3 && version(install.package_version) && strings(install.workflows) &&
+            install.workflows.every((id) => /^[a-z0-9]+(?:-[a-z0-9]+)*$/.test(id)) && new Set(install.workflows).size === install.workflows.length &&
+            install.managed_manifest === ".speculo/managed.json" && install.config_baseline_schema === 1;
+        add("install-contract", ok, ok ? "Speculo 1.x installation manifest valid" : "invalid installation manifest");
+        if (ok)
+            workflows = install.workflows;
+    }
+    const managed = await json(".speculo/managed.json");
+    if (managed) {
+        const ok = managed.schema_version === 2 && version(managed.package_version) && managed.package_version === install?.package_version && Array.isArray(managed.files) && managed.files.length > 0;
+        add("managed-contract", ok, ok ? "managed manifest schema v2 valid" : "invalid/empty managed manifest or package mismatch");
+        if (ok) {
+            const seen = new Set();
+            for (const file of managed.files) {
+                if (!record(file) || !safeRelativePath(file.path) || seen.has(file.path) || !/^[a-f0-9]{64}$/.test(String(file.sha256)) ||
+                    !Number.isSafeInteger(file.bytes) || Number(file.bytes) < 0 || !nonempty(file.owner) || !["static", "baseline", "contract"].includes(String(file.kind)) || !version(file.package_version)) {
+                    add("managed-entry", false, "invalid or duplicate managed file record");
+                    continue;
+                }
+                seen.add(file.path);
+                try {
+                    const actual = await sha256File(await containedPath(target, "speculo/" + file.path));
+                    if (actual.bytes !== file.bytes || actual.sha256 !== file.sha256)
+                        throw new Error("managed content differs from recorded digest; init replaces managed edits");
+                }
+                catch (error) {
+                    add("managed-file:" + file.path, false, String(error));
+                }
+            }
+            for (const required of ["commands/status.md", ".speculo/workspace.json", ".speculo/kernel.json", ".speculo/AGENTS.md", ".speculo/catalog.md"]) {
+                add("managed-required:" + required, seen.has(required), seen.has(required) ? "recorded" : "missing managed entry; refresh the installation");
+            }
+            add("managed-integrity", !checks.some((c) => !c.ok && /^(managed-entry|managed-file:|managed-required:)/.test(c.id)), `verified ${seen.size} declared files; runtime evidence is not overwritten`);
+        }
+    }
+    for (const workflow of workflows) {
+        const manifest = await json(`workflows/${workflow}/manifest.json`), contract = await json(`workflows/${workflow}/runtime-contract.json`);
+        try {
+            await readFile(await containedPath(target, `speculo/workflows/${workflow}/INDEX.md`));
+            const ok = manifest?.schema_version === 1 && manifest.id === workflow && Array.isArray(manifest.stages) && contract?.schema_version === 1 && contract.workflow === workflow;
+            add("workflow:" + workflow, ok, ok ? "entry, manifest and runtime contract present" : "workflow contract mismatch");
+        }
+        catch (error) {
+            add("workflow:" + workflow, false, String(error));
+        }
+    }
+    try {
+        const entries = await readdir(target);
+        if (entries.includes(LOCK_NAME)) {
+            let detail = "unidentified lock; inspect owner.json, do not automatically delete it";
+            try {
+                const j = await readTransaction(target);
+                detail = `transaction ${j.id}, phase ${j.phase}; after confirming its owner stopped: speculo recover ${JSON.stringify(target)} --transaction ${j.id}`;
+            }
+            catch (error) {
+                detail += "; " + String(error);
+            }
+            add("refresh-transaction", false, detail);
+        }
+        for (const name of entries.filter((name) => name.startsWith(".speculo-init-stage-") || name.startsWith(".speculo-file-")))
+            add("refresh-residue:" + name, false, "preserve residue; inspect transaction evidence before cleanup");
     }
-    const checkpointRoot = join(root, ".speculo", "context");
-    if (await pathExists(checkpointRoot)) {
-        checks.push({ id: "context-checkpoints", ok: true, message: "context directory present" });
+    catch (error) {
+        add("project-directory", false, String(error));
     }
-    return { target, healthy: checks.every((check) => check.ok), checks };
+    return { target, healthy: checks.every((c) => c.ok), scope: "installation-integrity", notChecked: ["domain-state-transitions", "live-service-health", "agent-behavior"], checks };
 }
 //# sourceMappingURL=doctor.js.map

package/dist/src/doctor.js.map

@@ -1 +1 @@
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