import { execFile } from "node:child_process";
import { createHash } from "node:crypto";
import {
  chmodSync, existsSync, mkdtempSync, mkdirSync, readdirSync, readFileSync, rmSync, symlinkSync, writeFileSync,
} from "node:fs";
import { tmpdir } from "node:os";
import { join } from "node:path";
import { promisify } from "node:util";
import { afterEach, expect, test } from "vitest";
import { WorkspaceRepositoryLock } from "../src/workspaces/git-repository.js";
import { WorkspaceRegistry } from "../src/workspaces/registry.js";
import {
  parseWorkspaceYaml, renderWorkspaceDocs, serializeWorkspaceYaml, type CanonicalWorkspace,
} from "../src/workspaces/schema.js";
import type { WorkspaceRegistryConfig } from "../src/workspaces/types.js";

const validYaml = `workspace:
  schema_version: 3
  id: psd-clinical
  name: Policlinico San Donato
  language: it
dwh:
  engine: postgres
  database: postgres
  schema: datawarehouse
  supported_transports: [postgres_direct]
semantic_index:
  vector_store:
    engine: qdrant
    collection: psd-clinical
    dimensions: 1024
    distance: cosine
  embedding:
    provider: ollama_internal
    model: qwen3-embedding:0.6b
    dimensions: 1024
llm_policy:
  allowed: [zai/glm-5.2]
`;

function withFilesystemEvidence(source: string, id = "psd-clinical"): string {
  return source.concat(`evidence:
  source:
    type: filesystem
    uri: workspace-content/${id}/evidence
`);
}

function withDwhRestTransport(source: string): string {
  return source.replace(
    "supported_transports: [postgres_direct]",
    "supported_transports: [postgres_direct, rest_api]",
  );
}

function withDwhRestDiagnostic(source: string): string {
  return withDwhRestTransport(source).concat(`diagnostics:
  dwh_rest:
    method: GET
    path: /health
    auth: none
    response:
      database: database
      schema: schema
`);
}

function withEmbeddingDiagnostic(source: string): string {
  return source.concat(`diagnostics:
  embedding:
    method: GET
    path: /models
    auth: none
    response:
      model: model
      dimensions: dimensions
`);
}

function withDwhRestAndEmbeddingDiagnostics(source: string): string {
  return withDwhRestTransport(source).concat(`diagnostics:
  dwh_rest:
    method: GET
    path: /health
    auth: none
    response:
      database: database
      schema: schema
  embedding:
    method: GET
    path: /models
    auth: none
    response:
      model: model
      dimensions: dimensions
`);
}

function withVectorRestTransport(source: string): string {
  return source.replace(
    "supported_transports: [pgvector_direct]",
    "supported_transports: [pgvector_direct, rest_api]",
  );
}

function withVectorMetadataDiagnostic(source: string): string {
  return withVectorRestTransport(source).concat(`diagnostics:
  vector_rest:
    metadata:
      method: GET
      path: /metadata
      auth: none
      response:
        collection: collection
        dimensions: dimensions
        distance: distance
`);
}

function withReversibleVectorProbe(source: string): string {
  return withVectorRestTransport(source).concat(`diagnostics:
  vector_rest:
    metadata:
      method: GET
      path: /metadata
      auth: none
      response:
        collection: collection
        dimensions: dimensions
        distance: distance
    reversible_probe:
      method: POST
      path: /probe
      auth: bearer
      response:
        operation: operation
`);
}

function legacyV1Yaml(source = validYaml): string {
  return source
    .replace("    engine: qdrant\n", "    engine: pgvector\n    database: postgres\n    schema: vectors\n")
    .replace("    collection: psd-clinical\n", "    collection: psd_clinical\n")
    .replace("    dimensions: 1024", "    dimensions: 768")
    .replace("    provider: ollama_internal", "    provider: ollama_compatible")
    .replace("    model: qwen3-embedding:0.6b", "    model: nomic-embed-text-v2-moe")
    .replace("    dimensions: 1024", "    dimensions: 768")
    .replace("distance: cosine\n", "distance: cosine\n    supported_transports: [pgvector_direct]\n")
    .replace("schema_version: 3", "schema_version: 1");
}

function legacyV2Yaml(source = validYaml): string {
  return source
    .replace("    engine: qdrant\n", "    engine: pgvector\n    database: postgres\n    schema: vectors\n")
    .replace("    collection: psd-clinical\n", "    collection: psd_clinical\n")
    .replace("    dimensions: 1024", "    dimensions: 768")
    .replace("    provider: ollama_internal", "    provider: ollama_compatible")
    .replace("    model: qwen3-embedding:0.6b", "    model: nomic-embed-text-v2-moe")
    .replace("    dimensions: 1024", "    dimensions: 768")
    .replace("distance: cosine\n", "distance: cosine\n    supported_transports: [pgvector_direct]\n")
    .replace("schema_version: 3", "schema_version: 2");
}

const runFile = promisify(execFile);
const temporaryRoots: string[] = [];

afterEach(() => {
  temporaryRoots.splice(0).forEach((root) => rmSync(root, { recursive: true, force: true }));
});

async function git(cwd: string, args: string[]): Promise<void> {
  await runFile("git", args, { cwd });
}

async function gitOutput(cwd: string, args: string[]): Promise<string> {
  const { stdout } = await runFile("git", args, { cwd });
  return stdout.trim();
}

async function fixture(workspaceSource = validYaml): Promise<{
  root: string; remote: string; source: string; initialCommit: string;
}> {
  const root = mkdtempSync(join(tmpdir(), "thoth-workspace-registry-"));
  temporaryRoots.push(root);
  const remote = join(root, "remote.git");
  const source = join(root, "source");
  await git(root, ["init", "--bare", "--initial-branch=main", remote]);
  mkdirSync(source);
  await git(source, ["init", "--initial-branch=main"]);
  await git(source, ["config", "user.name", "Workspace Registry Test"]);
  await git(source, ["config", "user.email", "workspace-registry@example.invalid"]);
  mkdirSync(join(source, "workspaces"));
  writeFileSync(join(source, "workspaces", "psd-clinical.yaml"), workspaceSource);
  if (workspaceSource.includes("type: filesystem")) {
    mkdirSync(join(source, "workspace-content", "psd-clinical", "evidence"), { recursive: true });
    mkdirSync(join(source, "workspace-content", "research", "evidence"), { recursive: true });
    writeFileSync(join(source, "workspace-content", "psd-clinical", "evidence", "guide.md"), "guide v1\n");
    writeFileSync(join(source, "workspace-content", "research", "evidence", "guide.md"), "research guide\n");
    await git(source, ["add", "workspaces", "workspace-content"]);
  } else {
    await git(source, ["add", "workspaces/psd-clinical.yaml"]);
  }
  await git(source, ["commit", "-m", "Initial workspace"]);
  await git(source, ["remote", "add", "origin", remote]);
  await git(source, ["push", "origin", "main"]);
  const { stdout } = await runFile("git", ["rev-parse", "HEAD"], { cwd: source });
  return { root, remote, source, initialCommit: stdout.trim() };
}

async function contentOnlyFixture(): Promise<{
  root: string; remote: string; source: string; initialCommit: string;
}> {
  const root = mkdtempSync(join(tmpdir(), "thoth-workspace-registry-empty-"));
  temporaryRoots.push(root);
  const remote = join(root, "remote.git");
  const source = join(root, "source");
  await git(root, ["init", "--bare", "--initial-branch=main", remote]);
  mkdirSync(source);
  await git(source, ["init", "--initial-branch=main"]);
  await git(source, ["config", "user.name", "Workspace Registry Test"]);
  await git(source, ["config", "user.email", "workspace-registry@example.invalid"]);
  const evidence = join(source, "workspace-content", "p1-filesystem", "evidence");
  mkdirSync(evidence, { recursive: true });
  writeFileSync(join(evidence, "guide.md"), "curated content\n");
  await git(source, ["add", "workspace-content"]);
  await git(source, ["commit", "-m", "Bootstrap curated content"]);
  await git(source, ["remote", "add", "origin", remote]);
  await git(source, ["push", "origin", "main"]);
  const initialCommit = await gitOutput(source, ["rev-parse", "HEAD"]);
  return { root, remote, source, initialCommit };
}

async function multiWorkspaceFixture(workspaces: Record<string, string>): Promise<{
  root: string; remote: string; source: string; initialCommit: string;
}> {
  const root = mkdtempSync(join(tmpdir(), "thoth-workspace-registry-"));
  temporaryRoots.push(root);
  const remote = join(root, "remote.git");
  const source = join(root, "source");
  await git(root, ["init", "--bare", "--initial-branch=main", remote]);
  mkdirSync(source);
  await git(source, ["init", "--initial-branch=main"]);
  await git(source, ["config", "user.name", "Workspace Registry Test"]);
  await git(source, ["config", "user.email", "workspace-registry@example.invalid"]);
  mkdirSync(join(source, "workspaces"));
  for (const [id, workspaceSource] of Object.entries(workspaces)) {
    writeFileSync(join(source, "workspaces", `${id}.yaml`), workspaceSource);
  }
  await git(source, ["add", "workspaces"]);
  await git(source, ["commit", "-m", "Initial workspaces"]);
  await git(source, ["remote", "add", "origin", remote]);
  await git(source, ["push", "origin", "main"]);
  const { stdout } = await runFile("git", ["rev-parse", "HEAD"], { cwd: source });
  return { root, remote, source, initialCommit: stdout.trim() };
}

function config(
  root: string,
  remoteUrl: string,
  overrides: Partial<WorkspaceRegistryConfig> = {},
): WorkspaceRegistryConfig {
  return {
    root,
    remoteUrl,
    branch: "main",
    gitAuthorName: "Workspace Registry Test",
    gitAuthorEmail: "workspace-registry@example.invalid",
    installationId: "test",
    secretRoots: [],
    maxImportBytes: 1024,
    maxImportEntries: 1,
    ...overrides,
  };
}

function workspaceWith(
  id: string,
  changes: Partial<Pick<CanonicalWorkspace["workspace"], "name" | "description">> = {},
): CanonicalWorkspace {
  const workspace = parseWorkspaceYaml(validYaml) as CanonicalWorkspace;
  return {
    ...workspace,
    workspace: { ...workspace.workspace, id, name: id, ...changes },
    semantic_index: {
      ...workspace.semantic_index,
      vector_store: { ...workspace.semantic_index.vector_store, collection: id },
    },
  };
}

function filesystemWorkspace(id: string): CanonicalWorkspace {
  return parseWorkspaceYaml(withFilesystemEvidence(
    validYaml
      .replace("id: psd-clinical", `id: ${id}`)
      .replace("name: Policlinico San Donato", `name: ${id}`)
      .replace("collection: psd-clinical", `collection: ${id}`),
    id,
  )) as CanonicalWorkspace;
}

async function checkoutStatus(checkout: string): Promise<{ porcelain: string; divergence: string }> {
  return {
    porcelain: await gitOutput(checkout, ["status", "--porcelain"]),
    divergence: await gitOutput(checkout, ["rev-list", "--left-right", "--count", "HEAD...@{upstream}"]),
  };
}

async function pushInvalidWorkspace(source: string): Promise<void> {
  writeFileSync(join(source, "workspaces", "psd-clinical.yaml"), "workspace: invalid\n");
  await git(source, ["add", "workspaces/psd-clinical.yaml"]);
  await git(source, ["commit", "-m", "Invalid workspace"]);
  await git(source, ["push", "origin", "main"]);
}

function legacyDigest(contents: string): string {
  return createHash("sha256").update(contents).digest("hex");
}

function persistPreStateManifest(root: string, commit: string): void {
  const snapshotDirectory = join(root, "snapshots", commit);
  const activePath = join(root, "state", "active.json");
  const snapshotPath = join(snapshotDirectory, "snapshot.json");
  const active = JSON.parse(readFileSync(activePath, "utf8"));
  const manifest = JSON.parse(readFileSync(snapshotPath, "utf8"));
  const envName = "psd-clinical.env.example";
  const docsName = "psd-clinical.md";
  const envExample = "# Legacy registry artifact\n";
  const markdown = "# Legacy registry artifact\n";

  chmodSync(join(snapshotDirectory, envName), 0o600);
  chmodSync(join(snapshotDirectory, docsName), 0o600);
  writeFileSync(join(snapshotDirectory, envName), envExample);
  writeFileSync(join(snapshotDirectory, docsName), markdown);
  active.revisions = active.revisions.map(({ state: _state, ...revision }: Record<string, unknown>) => revision);
  manifest.revisions = manifest.revisions.map(({ state: _state, ...revision }: Record<string, unknown>) => revision);
  manifest.files = {
    "psd-clinical.yaml": manifest.files["psd-clinical.yaml"],
    [envName]: legacyDigest(envExample),
    [docsName]: legacyDigest(markdown),
  };
  writeFileSync(activePath, JSON.stringify(active));
  chmodSync(snapshotPath, 0o600);
  writeFileSync(snapshotPath, JSON.stringify(manifest));
}

test("allows first API publication and delete-last from a content-only registry base", async () => {
  const remote = await contentOnlyFixture();
  const registry = new WorkspaceRegistry(config(join(remote.root, "registry"), remote.remote));

  await expect(registry.bootstrap()).resolves.toMatchObject({ head: remote.initialCommit });
  await expect(registry.list()).resolves.toEqual([]);

  const created = await registry.publish({
    action: "create",
    workspace: filesystemWorkspace("p1-filesystem"),
    baseCommit: remote.initialCommit,
  });
  expect(created).toMatchObject({ id: "p1-filesystem" });

  await expect(registry.publish({
    action: "delete",
    id: "p1-filesystem",
    baseCommit: created!.commit,
    baseBlob: created!.blob,
  })).resolves.toBeUndefined();
  await expect(registry.list()).resolves.toEqual([]);
});

test("bootstraps a checkout and activates a validated immutable snapshot", async () => {
  const remote = await fixture();
  const registry = new WorkspaceRegistry(config(join(remote.root, "registry"), remote.remote));

  const status = await registry.bootstrap();

  expect(status.head).toMatch(/^[0-9a-f]{40}$/);
  expect(existsSync(registry.snapshotPath(status.head!, "psd-clinical"))).toBe(true);
  await expect(registry.read("psd-clinical")).resolves.toMatchObject({
    revision: { commit: remote.initialCommit, id: "psd-clinical" },
  });
});

test("concurrent first lists lazily bootstrap a clean registry once safely", async () => {
  const remote = await fixture();
  const root = join(remote.root, "registry");
  const registry = new WorkspaceRegistry(config(root, remote.remote));

  const [first, second] = await Promise.all([registry.list(), registry.list()]);
  for (const revisions of [first, second]) {
    expect(revisions).toEqual([
      expect.objectContaining({
        id: "psd-clinical",
        commit: remote.initialCommit,
        state: "operational",
      }),
    ]);
  }
  expect(existsSync(join(root, "state", "active.json"))).toBe(true);
});

test("publishes a filesystem descriptor only when its Evidence tree exists in the pulled base", async () => {
  const remote = await fixture(withFilesystemEvidence(validYaml));
  const root = join(remote.root, "registry");
  const registry = new WorkspaceRegistry(config(root, remote.remote));
  await registry.bootstrap();
  const evidencePath = "workspace-content/research/evidence";
  const initialTree = await gitOutput(remote.root, [
    "--git-dir", remote.remote, "rev-parse", `${remote.initialCommit}:${evidencePath}`,
  ]);

  const created = await registry.publish({
    action: "create",
    workspace: filesystemWorkspace("research"),
    baseCommit: remote.initialCommit,
  });

  expect(created?.commit).not.toBe(remote.initialCommit);
  await expect(runFile("git", [
    "--git-dir", remote.remote, "cat-file", "-e", `${created!.commit}:workspaces/research.yaml`,
  ], { cwd: remote.root })).resolves.toBeDefined();
  await expect(runFile("git", [
    "--git-dir", remote.remote, "cat-file", "-e", `${created!.commit}:${evidencePath}/guide.md`,
  ], { cwd: remote.root })).resolves.toBeDefined();
  expect(await gitOutput(remote.root, [
    "--git-dir", remote.remote, "rev-parse", `${created!.commit}:${evidencePath}`,
  ])).toBe(initialTree);

  const remoteHeadBeforeMissing = await gitOutput(remote.root, ["--git-dir", remote.remote, "rev-parse", "HEAD"]);
  await expect(registry.publish({
    action: "create",
    workspace: filesystemWorkspace("missing-tree"),
    baseCommit: created!.commit,
  })).rejects.toMatchObject({ code: "workspace_invalid" });
  expect(await gitOutput(remote.root, ["--git-dir", remote.remote, "rev-parse", "HEAD"])).toBe(
    remoteHeadBeforeMissing,
  );
  expect(await checkoutStatus(join(root, "repo"))).toEqual({ porcelain: "", divergence: "0\t0" });
});

test.each(["missing", "blob"])(
  "rejects a remote filesystem descriptor with a %s Evidence root and keeps the active snapshot",
  async (invalidKind) => {
    const remote = await fixture(withFilesystemEvidence(validYaml));
    const registry = new WorkspaceRegistry(config(join(remote.root, "registry"), remote.remote));
    await registry.bootstrap();
    const evidenceRoot = join(remote.source, "workspace-content", "psd-clinical", "evidence");
    rmSync(evidenceRoot, { recursive: true, force: true });
    if (invalidKind === "blob") writeFileSync(evidenceRoot, "not a tree\n");
    await git(remote.source, ["add", "-A", "workspace-content/psd-clinical/evidence"]);
    await git(remote.source, ["commit", "-m", `Make Evidence root ${invalidKind}`]);
    await git(remote.source, ["push", "origin", "main"]);
    const invalidCommit = await gitOutput(remote.source, ["rev-parse", "HEAD"]);

    await expect(registry.pull()).rejects.toMatchObject({ code: "workspace_invalid" });
    expect(invalidCommit).not.toBe(remote.initialCommit);
    await expect(registry.read("psd-clinical")).resolves.toMatchObject({
      revision: { commit: remote.initialCommit },
    });
  },
);

test("activation validates filesystem Evidence against its exact safeHead rather than checkout HEAD", async () => {
  const remote = await fixture(withFilesystemEvidence(validYaml));
  const registry = new WorkspaceRegistry(config(join(remote.root, "registry"), remote.remote));
  await registry.bootstrap();
  rmSync(join(remote.source, "workspace-content", "psd-clinical", "evidence"), {
    recursive: true, force: true,
  });
  await git(remote.source, ["add", "-A", "workspace-content/psd-clinical/evidence"]);
  await git(remote.source, ["commit", "-m", "Remove current Evidence root"]);
  await git(remote.source, ["push", "origin", "main"]);
  const invalidHead = await gitOutput(remote.source, ["rev-parse", "HEAD"]);
  const internals = registry as unknown as {
    repository: { pull(): Promise<{ head?: string }> };
    activate(commit: string): Promise<void>;
  };

  expect((await internals.repository.pull()).head).toBe(invalidHead);
  await expect(internals.activate(remote.initialCommit)).resolves.toBeUndefined();
  await expect(registry.read("psd-clinical")).resolves.toMatchObject({
    revision: { commit: remote.initialCommit },
  });
});

test("creates an immutable descriptor revision for a content-only Evidence commit", async () => {
  const remote = await fixture(withFilesystemEvidence(validYaml));
  const root = join(remote.root, "registry");
  const registry = new WorkspaceRegistry(config(root, remote.remote));
  await registry.bootstrap();
  const initial = await registry.read("psd-clinical");
  const evidencePath = "workspace-content/psd-clinical/evidence";
  const initialTree = await gitOutput(remote.source, ["rev-parse", `${remote.initialCommit}:${evidencePath}`]);
  writeFileSync(join(remote.source, evidencePath, "guide.md"), "guide v2\n");
  await git(remote.source, ["add", `${evidencePath}/guide.md`]);
  await git(remote.source, ["commit", "-m", "Update Evidence only"]);
  await git(remote.source, ["push", "origin", "main"]);
  const contentCommit = await gitOutput(remote.source, ["rev-parse", "HEAD"]);
  const contentTree = await gitOutput(remote.source, ["rev-parse", `${contentCommit}:${evidencePath}`]);

  await registry.pull();
  const current = await registry.read("psd-clinical");

  expect(contentTree).not.toBe(initialTree);
  expect(current.revision).toMatchObject({ commit: contentCommit, blob: initial.revision.blob });
  expect(current.revision.snapshotPath).not.toBe(initial.revision.snapshotPath);
  expect(readFileSync(current.revision.snapshotPath, "utf8")).toBe(
    readFileSync(initial.revision.snapshotPath, "utf8"),
  );
  await expect(runFile("git", [
    "--git-dir", remote.remote, "cat-file", "-e", `${contentCommit}:${evidencePath}/guide.md`,
  ], { cwd: remote.root })).resolves.toBeDefined();
});

test("rejects a stale API update after a content-only Evidence commit", async () => {
  const remote = await fixture(withFilesystemEvidence(validYaml));
  const registry = new WorkspaceRegistry(config(join(remote.root, "registry"), remote.remote));
  await registry.bootstrap();
  const initial = await registry.read("psd-clinical");
  const guide = join(remote.source, "workspace-content", "psd-clinical", "evidence", "guide.md");
  writeFileSync(guide, "curator content\n");
  await git(remote.source, ["add", "workspace-content/psd-clinical/evidence/guide.md"]);
  await git(remote.source, ["commit", "-m", "Curator Evidence update"]);
  await git(remote.source, ["push", "origin", "main"]);
  const curatorCommit = await gitOutput(remote.source, ["rev-parse", "HEAD"]);

  await expect(registry.publish({
    action: "update",
    workspace: filesystemWorkspace("psd-clinical"),
    baseCommit: initial.revision.commit,
    baseBlob: initial.revision.blob,
  })).rejects.toMatchObject({ code: "workspace_stale" });
  expect(await gitOutput(remote.root, ["--git-dir", remote.remote, "rev-parse", "HEAD"])).toBe(curatorCommit);
});

test("keeps content-only historical descriptor revisions distinguishable by commit", async () => {
  const remote = await fixture(withFilesystemEvidence(validYaml));
  const registry = new WorkspaceRegistry(config(join(remote.root, "registry"), remote.remote));
  await registry.bootstrap();
  writeFileSync(
    join(remote.source, "workspace-content", "psd-clinical", "evidence", "guide.md"),
    "historical content\n",
  );
  await git(remote.source, ["add", "workspace-content/psd-clinical/evidence/guide.md"]);
  await git(remote.source, ["commit", "-m", "Retained Evidence update"]);
  await git(remote.source, ["push", "origin", "main"]);
  const contentCommit = await gitOutput(remote.source, ["rev-parse", "HEAD"]);
  await registry.pull();
  await registry.reconcileSnapshotRetention([remote.initialCommit]);

  const retained = (await registry.listRetainedSnapshots()).filter(({ id }) => id === "psd-clinical");
  expect(retained.map(({ commit }) => commit)).toEqual([contentCommit, remote.initialCommit]);
  const oldPinned = await registry.readPinned("psd-clinical", remote.initialCommit);
  const newPinned = await registry.readPinned("psd-clinical", contentCommit);
  expect(oldPinned.workspaceConfigPath).not.toBe(newPinned.workspaceConfigPath);
  expect(oldPinned.workspace).toEqual(newPinned.workspace);
});

test("publishes create, update, and delete with the configured Git author identity", async () => {
  const remote = await fixture();
  const registry = new WorkspaceRegistry(config(join(remote.root, "registry"), remote.remote, {
    gitAuthorName: "Configured Workspace Publisher",
    gitAuthorEmail: "publisher@example.invalid",
  }));
  await registry.bootstrap();
  const createdWorkspace = workspaceWith("research-registry", { name: "Research registry" });

  const created = await registry.publish({
    action: "create",
    workspace: createdWorkspace,
    baseCommit: remote.initialCommit,
  });

  expect(created).toMatchObject({ id: "research-registry", commit: expect.stringMatching(/^[0-9a-f]{40}$/) });
  expect(await gitOutput(remote.root, ["--git-dir", remote.remote, "log", "-1", "--format=%an <%ae>"])).toBe(
    "Configured Workspace Publisher <publisher@example.invalid>",
  );
  await expect(runFile("git", ["--git-dir", remote.remote, "cat-file", "-e", "HEAD:workspace-docs/research-registry/README.md"], {
    cwd: remote.root,
  })).resolves.toBeDefined();

  const updated = await registry.publish({
    action: "update",
    workspace: workspaceWith("research-registry", { description: "Updated workspace description" }),
    baseCommit: created!.commit,
    baseBlob: created!.blob,
  });

  expect(updated).toMatchObject({ id: "research-registry" });
  expect(await gitOutput(remote.root, ["--git-dir", remote.remote, "show", "HEAD:workspaces/research-registry.yaml"])).toContain(
    "description: Updated workspace description",
  );

  await expect(registry.publish({
    action: "delete",
    id: "research-registry",
    baseCommit: updated!.commit,
    baseBlob: updated!.blob,
  })).resolves.toBeUndefined();
  await expect(runFile("git", ["--git-dir", remote.remote, "cat-file", "-e", "HEAD:workspaces/research-registry.yaml"], {
    cwd: remote.root,
  })).rejects.toBeDefined();
});

test("reports stale publish conflicts with expected and actual revisions", async () => {
  const remote = await fixture();
  const root = join(remote.root, "registry");
  const registry = new WorkspaceRegistry(config(root, remote.remote));
  await registry.bootstrap();
  const initial = await registry.read("psd-clinical");
  writeFileSync(join(remote.source, "workspaces", "psd-clinical.yaml"), validYaml.replace(
    "schema: datawarehouse", "schema: analytics",
  ));
  await git(remote.source, ["add", "workspaces/psd-clinical.yaml"]);
  await git(remote.source, ["commit", "-m", "Change dwh schema"]);
  await git(remote.source, ["push", "origin", "main"]);
  const actualCommit = await gitOutput(remote.source, ["rev-parse", "HEAD"]);
  const actualBlob = await gitOutput(remote.source, ["rev-parse", "HEAD:workspaces/psd-clinical.yaml"]);

  await expect(registry.publish({
    action: "update",
    workspace: workspaceWith("psd-clinical", { description: "Local stale change" }),
    baseCommit: initial.revision.commit,
    baseBlob: initial.revision.blob,
  })).rejects.toMatchObject({
    code: "workspace_conflict",
    fields: ["dwh.schema"],
    expected: { commit: initial.revision.commit, blob: initial.revision.blob },
    actual: { commit: actualCommit, blob: actualBlob },
  });
});

test.each([
  ["adds", validYaml, withDwhRestDiagnostic(validYaml)],
  ["removes", withDwhRestDiagnostic(validYaml), validYaml],
])("reports an optional diagnostics branch when the registry %s it", async (_operation, baseSource, remoteSource) => {
  const remote = await fixture(baseSource);
  const registry = new WorkspaceRegistry(config(join(remote.root, "registry"), remote.remote));
  await registry.bootstrap();
  const initial = await registry.read("psd-clinical");
  writeFileSync(join(remote.source, "workspaces", "psd-clinical.yaml"), remoteSource);
  await git(remote.source, ["add", "workspaces/psd-clinical.yaml"]);
  await git(remote.source, ["commit", "-m", `Registry ${_operation} diagnostic branch`]);
  await git(remote.source, ["push", "origin", "main"]);

  await expect(registry.publish({
    action: "update",
    workspace: workspaceWith("psd-clinical", { description: "Local stale change" }),
    baseCommit: initial.revision.commit,
    baseBlob: initial.revision.blob,
  })).rejects.toMatchObject({
    code: "workspace_conflict",
    fields: ["dwh.supported_transports", "diagnostics"],
  });
});

test("restores a clean checkout after a failed commit and retries publication", async () => {
  const remote = await fixture();
  const root = join(remote.root, "registry");
  const registry = new WorkspaceRegistry(config(root, remote.remote));
  await registry.bootstrap();
  const objects = join(root, "repo", ".git", "objects");
  chmodSync(objects, 0o500);
  const request = {
    action: "create" as const,
    workspace: workspaceWith("commit-recovery"),
    baseCommit: remote.initialCommit,
  };

  try {
    await expect(registry.publish(request)).rejects.toMatchObject({ code: "git_unavailable" });
  } finally {
    chmodSync(objects, 0o700);
  }
  expect(await checkoutStatus(join(root, "repo"))).toEqual({ porcelain: "", divergence: "0\t0" });
  await expect(registry.pull()).resolves.toMatchObject({ head: remote.initialCommit });
  await expect(registry.publish(request)).resolves.toMatchObject({ id: "commit-recovery" });
});

test("resets an ahead checkout after a rejected push and retries publication", async () => {
  const remote = await fixture();
  const root = join(remote.root, "registry");
  const registry = new WorkspaceRegistry(config(root, remote.remote));
  await registry.bootstrap();
  const hook = join(remote.remote, "hooks", "pre-receive");
  writeFileSync(hook, "#!/bin/sh\nexit 1\n", { mode: 0o755 });
  const request = {
    action: "create" as const,
    workspace: workspaceWith("push-recovery"),
    baseCommit: remote.initialCommit,
  };

  await expect(registry.publish(request)).rejects.toMatchObject({ code: "git_push_rejected" });
  expect(await checkoutStatus(join(root, "repo"))).toEqual({ porcelain: "", divergence: "0\t0" });
  rmSync(hook);
  await expect(registry.pull()).resolves.toMatchObject({ head: remote.initialCommit });
  await expect(registry.publish(request)).resolves.toMatchObject({ id: "push-recovery" });
});

test.each([
  ["v1", legacyV1Yaml()],
  ["v2", legacyV2Yaml()],
])("rejects a schema %s descriptor instead of activating it", async (_version, legacyYaml) => {
  const remote = await fixture(legacyYaml);
  const registry = new WorkspaceRegistry(config(join(remote.root, "registry"), remote.remote));

  await expect(registry.bootstrap()).rejects.toMatchObject({ code: "workspace_invalid" });
  expect(existsSync(join(remote.root, "registry", "state", "active.json"))).toBe(false);
});

test("migrates a validated pre-state manifest while preserving its v3 operational state", async () => {
  const remote = await fixture();
  const root = join(remote.root, "registry");
  const firstRegistry = new WorkspaceRegistry(config(root, remote.remote));
  await firstRegistry.bootstrap();
  persistPreStateManifest(root, remote.initialCommit);

  const restoredRegistry = new WorkspaceRegistry(config(root, remote.remote));
  await expect(restoredRegistry.bootstrap()).resolves.toMatchObject({
    head: remote.initialCommit,
    degraded: false,
  });
  await expect(restoredRegistry.list()).resolves.toMatchObject([
    { id: "psd-clinical", state: "operational" },
  ]);

  const active = JSON.parse(readFileSync(join(root, "state", "active.json"), "utf8"));
  const manifest = JSON.parse(readFileSync(join(root, "snapshots", remote.initialCommit, "snapshot.json"), "utf8"));
  expect(active.revisions[0].state).toBe("operational");
  expect(manifest.revisions[0].state).toBe("operational");
  expect(Object.keys(manifest.files).sort()).toEqual([
    "psd-clinical.env.example", "psd-clinical.md", "psd-clinical.yaml",
  ]);
});

test("finishes a pre-state active manifest migration after its v3 snapshot was atomically updated", async () => {
  const remote = await fixture();
  const root = join(remote.root, "registry");
  const registry = new WorkspaceRegistry(config(root, remote.remote));
  await registry.bootstrap();
  persistPreStateManifest(root, remote.initialCommit);

  const snapshotPath = join(root, "snapshots", remote.initialCommit, "snapshot.json");
  const manifest = JSON.parse(readFileSync(snapshotPath, "utf8"));
  manifest.revisions[0].state = "operational";
  writeFileSync(snapshotPath, JSON.stringify(manifest));

  const restoredRegistry = new WorkspaceRegistry(config(root, remote.remote));
  await expect(restoredRegistry.list()).resolves.toMatchObject([
    { id: "psd-clinical", state: "operational" },
  ]);
});

test("rejects a corrupt pre-state manifest rather than accepting it during migration", async () => {
  const remote = await fixture();
  const root = join(remote.root, "registry");
  const registry = new WorkspaceRegistry(config(root, remote.remote));
  await registry.bootstrap();
  persistPreStateManifest(root, remote.initialCommit);
  const snapshotPath = join(root, "snapshots", remote.initialCommit, "snapshot.json");
  const manifest = JSON.parse(readFileSync(snapshotPath, "utf8"));
  manifest.files["psd-clinical.yaml"] = "0".repeat(64);
  writeFileSync(snapshotPath, JSON.stringify(manifest));

  const restoredRegistry = new WorkspaceRegistry(config(root, remote.remote));
  await expect(restoredRegistry.bootstrap()).rejects.toMatchObject({ code: "workspace_invalid" });
  await expect(restoredRegistry.list()).rejects.toMatchObject({ code: "workspace_invalid" });
});

test("keeps the last valid snapshot when a pulled commit has invalid YAML", async () => {
  const remote = await fixture();
  const registry = new WorkspaceRegistry(config(join(remote.root, "registry"), remote.remote));
  await registry.bootstrap();
  await pushInvalidWorkspace(remote.source);

  await expect(registry.pull()).rejects.toMatchObject({ code: "workspace_invalid" });
  await expect(registry.read("psd-clinical")).resolves.toMatchObject({
    revision: { commit: remote.initialCommit },
  });
});

test("rejects duplicate schema v3 collection ownership and keeps the previous active snapshot", async () => {
  const v3Yaml = validYaml;
  const remote = await multiWorkspaceFixture({
    "psd-clinical": v3Yaml,
    "research-clinical": v3Yaml
      .replace("id: psd-clinical", "id: research-clinical")
      .replace("name: Policlinico San Donato", "name: Research Clinical")
      .replace("collection: psd-clinical", "collection: research-clinical"),
  });
  const registry = new WorkspaceRegistry(config(join(remote.root, "registry"), remote.remote));
  await registry.bootstrap();

  writeFileSync(
    join(remote.source, "workspaces", "research-clinical.yaml"),
    v3Yaml
      .replace("id: psd-clinical", "id: research-clinical")
      .replace("name: Policlinico San Donato", "name: Research Clinical")
      .replace("collection: psd-clinical", "collection: shared"),
  );
  writeFileSync(
    join(remote.source, "workspaces", "psd-clinical.yaml"),
    v3Yaml.replace("collection: psd-clinical", "collection: shared"),
  );
  await git(remote.source, ["add", "workspaces"]);
  await git(remote.source, ["commit", "-m", "Duplicate collection ownership"]);
  await git(remote.source, ["push", "origin", "main"]);

  await expect(registry.pull()).rejects.toMatchObject({
    code: "workspace_invalid",
    message: "Workspace repository content is invalid",
  });
  await expect(registry.read("psd-clinical")).resolves.toMatchObject({
    revision: { commit: remote.initialCommit },
  });
  await expect(registry.read("research-clinical")).resolves.toMatchObject({
    revision: { commit: remote.initialCommit },
  });
});

test("retains a historical snapshot while a resumable manifest still references its revision", async () => {
  const remote = await fixture();
  const root = join(remote.root, "registry");
  const registry = new WorkspaceRegistry(config(root, remote.remote));
  await registry.bootstrap();

  writeFileSync(join(remote.source, "workspaces", "psd-clinical.yaml"), validYaml.replace(
    "name: Policlinico San Donato", "name: Updated Policlinico San Donato",
  ));
  await git(remote.source, ["add", "workspaces/psd-clinical.yaml"]);
  await git(remote.source, ["commit", "-m", "Update workspace"]);
  await git(remote.source, ["push", "origin", "main"]);
  const currentCommit = await gitOutput(remote.source, ["rev-parse", "HEAD"]);
  await registry.pull();

  await registry.reconcileSnapshotRetention([remote.initialCommit]);
  expect(existsSync(registry.snapshotPath(remote.initialCommit, "psd-clinical"))).toBe(true);
  expect(existsSync(registry.snapshotPath(currentCommit, "psd-clinical"))).toBe(true);

  await registry.reconcileSnapshotRetention([]);
  expect(existsSync(registry.snapshotPath(remote.initialCommit, "psd-clinical"))).toBe(false);
  expect(existsSync(registry.snapshotPath(currentCommit, "psd-clinical"))).toBe(true);
});

test("a session revision lease survives stale retention scans until its manifest is observed", async () => {
  const remote = await fixture();
  const root = join(remote.root, "registry");
  const registry = new WorkspaceRegistry(config(root, remote.remote));
  await registry.bootstrap();
  const lease = await registry.acquireSessionRevision("psd-clinical");

  writeFileSync(join(remote.source, "workspaces", "psd-clinical.yaml"), validYaml.replace(
    "name: Policlinico San Donato", "name: Concurrent revision",
  ));
  await git(remote.source, ["add", "workspaces/psd-clinical.yaml"]);
  await git(remote.source, ["commit", "-m", "Publish while session is starting"]);
  await git(remote.source, ["push", "origin", "main"]);
  await registry.pull();

  await registry.reconcileSnapshotRetention([]);
  expect(existsSync(registry.snapshotPath(remote.initialCommit, "psd-clinical"))).toBe(true);

  await lease.markPersisted();
  await registry.reconcileSnapshotRetention([]);
  expect(existsSync(registry.snapshotPath(remote.initialCommit, "psd-clinical"))).toBe(true);

  await registry.reconcileSnapshotRetention([remote.initialCommit]);
  await registry.reconcileSnapshotRetention([]);
  expect(existsSync(registry.snapshotPath(remote.initialCommit, "psd-clinical"))).toBe(false);
});

test("lists operational descriptors retained after their workspace was removed from the active revision", async () => {
  const remote = await fixture();
  const root = join(remote.root, "registry");
  const registry = new WorkspaceRegistry(config(root, remote.remote));
  await registry.bootstrap();

  writeFileSync(join(remote.source, "workspaces", "archive-only.yaml"), validYaml.replace(
    "id: psd-clinical", "id: archive-only",
  ).replace("collection: psd-clinical", "collection: archive-only"));
  await git(remote.source, ["add", "workspaces/archive-only.yaml"]);
  await git(remote.source, ["commit", "-m", "Add retained workspace"]);
  await git(remote.source, ["push", "origin", "main"]);
  await registry.pull();

  rmSync(join(remote.source, "workspaces", "psd-clinical.yaml"));
  await git(remote.source, ["add", "-u"]);
  await git(remote.source, ["commit", "-m", "Remove original workspace"]);
  await git(remote.source, ["push", "origin", "main"]);
  await registry.pull();

  const retained = await registry.listRetainedSnapshots();
  expect(retained).toEqual(expect.arrayContaining([
    expect.objectContaining({ id: "psd-clinical", commit: remote.initialCommit, state: "operational" }),
    expect.objectContaining({ id: "archive-only", state: "operational" }),
  ]));
});

test("does not bypass an existing live advisory repository lock", async () => {
  const remote = await fixture();
  const root = join(remote.root, "registry");
  const registry = new WorkspaceRegistry(config(root, remote.remote));
  const lock = new WorkspaceRepositoryLock(join(root, "locks"));
  let release!: () => void;
  let started!: () => void;
  const held = lock.run(async () => {
    started();
    await new Promise<void>((resolve) => { release = resolve; });
  });
  await new Promise<void>((resolve) => { started = resolve; });

  try {
    await expect(registry.bootstrap()).rejects.toMatchObject({ code: "workspace_stale" });
  } finally {
    release();
    await held;
  }
});

test("rejects a symbolic-link registry root before creating a lock below it", async () => {
  const remote = await fixture();
  const target = join(remote.root, "registry-target");
  const root = join(remote.root, "registry-link");
  mkdirSync(target);
  symlinkSync(target, root);
  const registry = new WorkspaceRegistry(config(root, remote.remote));

  await expect(registry.bootstrap()).rejects.toMatchObject({ code: "git_unavailable" });
  expect(existsSync(join(target, "locks"))).toBe(false);
});

test("rejects a locally-ahead checkout instead of activating local-only content", async () => {
  const remote = await fixture();
  const root = join(remote.root, "registry");
  const registry = new WorkspaceRegistry(config(root, remote.remote));
  await registry.bootstrap();
  const checkout = join(root, "repo");
  writeFileSync(join(checkout, "workspaces", "psd-clinical.yaml"), validYaml.replace(
    "name: Policlinico San Donato", "name: Local only workspace",
  ));
  await git(checkout, ["config", "user.name", "Workspace Registry Test"]);
  await git(checkout, ["config", "user.email", "workspace-registry@example.invalid"]);
  await git(checkout, ["add", "workspaces/psd-clinical.yaml"]);
  await git(checkout, ["commit", "-m", "Local-only workspace"]);

  await expect(registry.pull()).rejects.toMatchObject({ code: "git_non_fast_forward" });
  await expect(registry.read("psd-clinical")).resolves.toMatchObject({
    revision: { commit: remote.initialCommit },
    workspace: { workspace: { name: "Policlinico San Donato" } },
  });
});

test("recovers a dead-process advisory lock while preserving active snapshot safety", async () => {
  const remote = await fixture();
  const root = join(remote.root, "registry");
  mkdirSync(join(root, "locks"), { recursive: true });
  writeFileSync(join(root, "locks", "repository.lock"), JSON.stringify({ pid: 999_999_999 }));
  const registry = new WorkspaceRegistry(config(root, remote.remote));

  await expect(registry.bootstrap()).resolves.toMatchObject({
    head: remote.initialCommit,
    degraded: false,
  });
});

test.each(["manifest", "blob", "workspace", "document"])(
  "rejects a corrupted %s snapshot component instead of reporting it active",
  async (component) => {
    const remote = await fixture();
    const root = join(remote.root, "registry");
    const registry = new WorkspaceRegistry(config(root, remote.remote));
    await registry.bootstrap();
    const snapshot = join(root, "snapshots", remote.initialCommit);

    if (component === "manifest") {
      const file = join(snapshot, "snapshot.json");
      chmodSync(file, 0o600);
      writeFileSync(file, "{");
    }
    if (component === "blob") {
      const activePath = join(root, "state", "active.json");
      const active = JSON.parse(readFileSync(activePath, "utf8"));
      active.revisions[0].blob = "not-a-git-blob";
      writeFileSync(activePath, JSON.stringify(active));
    }
    if (component === "workspace") {
      const file = join(snapshot, "psd-clinical.yaml");
      chmodSync(file, 0o600);
      writeFileSync(file, "truncated");
    }
    if (component === "document") rmSync(join(snapshot, "psd-clinical.md"));

    await expect(registry.list()).rejects.toMatchObject({ code: "workspace_invalid" });
    await expect(registry.read("psd-clinical")).rejects.toMatchObject({ code: "workspace_invalid" });
  },
);

test("rejects a corrupt fallback snapshot instead of returning degraded active state", async () => {
  const remote = await fixture();
  const root = join(remote.root, "registry");
  const registry = new WorkspaceRegistry(config(root, remote.remote));
  await registry.bootstrap();
  const document = join(root, "snapshots", remote.initialCommit, "psd-clinical.md");
  chmodSync(document, 0o600);
  writeFileSync(document, "corrupt");
  rmSync(remote.remote, { recursive: true, force: true });

  await expect(registry.pull()).rejects.toMatchObject({ code: "workspace_invalid" });
});


test("snapshots canonical Evidence artifacts at the active commit without copying Evidence bytes", async () => {
  const remote = await fixture(withFilesystemEvidence(validYaml));
  const registryRoot = join(remote.root, "registry");
  const registry = new WorkspaceRegistry(config(registryRoot, remote.remote));

  const status = await registry.bootstrap();
  const active = await registry.read("psd-clinical");
  const snapshotDirectory = join(registryRoot, "snapshots", status.head!);
  const descriptor = active.workspace as CanonicalWorkspace;
  const docs = renderWorkspaceDocs(descriptor);
  const expectedFiles: Record<string, string> = {
    "psd-clinical.yaml": serializeWorkspaceYaml(descriptor),
    "psd-clinical.env.example": docs.envExample,
    "psd-clinical.md": docs.markdown,
  };
  const manifest = JSON.parse(readFileSync(join(snapshotDirectory, "snapshot.json"), "utf8"));

  expect(status.head).toBe(remote.initialCommit);
  const committedDescriptor = parseWorkspaceYaml(await gitOutput(remote.source, [
    "show", `${remote.initialCommit}:workspaces/psd-clinical.yaml`,
  ])) as CanonicalWorkspace;
  const committedBlob = await gitOutput(remote.source, [
    "rev-parse", `${remote.initialCommit}:workspaces/psd-clinical.yaml`,
  ]);
  expect(active.revision.blob).toBe(committedBlob);
  expect(expectedFiles["psd-clinical.yaml"]).toBe(serializeWorkspaceYaml(committedDescriptor));
  expect(readdirSync(snapshotDirectory).sort()).toEqual([
    "psd-clinical.env.example", "psd-clinical.md", "psd-clinical.yaml", "snapshot.json",
  ]);
  expect(manifest.head).toBe(remote.initialCommit);
  expect(manifest.revisions[0]).toMatchObject({
    id: "psd-clinical", commit: remote.initialCommit, blob: committedBlob,
  });
  expect(Object.keys(manifest.files).sort()).toEqual(Object.keys(expectedFiles).sort());
  for (const [name, contents] of Object.entries(expectedFiles)) {
    expect(readFileSync(join(snapshotDirectory, name), "utf8")).toBe(contents);
    expect(manifest.files[name]).toBe(createHash("sha256").update(contents).digest("hex"));
  }
  expect(JSON.stringify(manifest)).not.toContain("workspace-content/");
  expect(readdirSync(snapshotDirectory).some((name) => name === "workspace-content")).toBe(false);
  expect(readFileSync(join(remote.source, "workspace-content/psd-clinical/evidence/guide.md"), "utf8"))
    .toBe("guide v1\n");
});

test("never copies an installation secret canary into Git, generated artifacts, metadata, or errors", async () => {
  const remote = await fixture(validYaml.concat(`evidence:
  source:
    type: http
    uris: [https://evidence.example.test/guide.md]
    authentication: signed_urls_file
`));
  const canary = "CANARY-EVIDENCE-SECRET-ONLY-IN-FIXTURE";
  const secretDirectory = join(remote.root, "fixture-secrets");
  mkdirSync(secretDirectory);
  const secretFile = join(secretDirectory, "signed-urls");
  writeFileSync(secretFile, canary);
  const registryRoot = join(remote.root, "registry");
  const registry = new WorkspaceRegistry(config(registryRoot, remote.remote, {
    secretRoots: [secretDirectory],
  }));
  const previous = process.env.THT_WS_PSD_CLINICAL_EVIDENCE_SIGNED_URLS_FILE;
  process.env.THT_WS_PSD_CLINICAL_EVIDENCE_SIGNED_URLS_FILE = secretFile;
  try {
    const status = await registry.bootstrap();
    const snapshotDirectory = join(registryRoot, "snapshots", status.head!);
    let gitBlobText = "";
    try {
      gitBlobText = (await runFile(
        "git", ["grep", "-I", "-h", "-e", canary, "HEAD", "--", "."], { cwd: remote.source },
      )).stdout;
    } catch (error) {
      if (!error || typeof error !== "object" || !("code" in error) || error.code !== 1) throw error;
      gitBlobText = "stdout" in error ? String(error.stdout ?? "") : "";
    }
    expect(gitBlobText).toBe("");
    for (const name of readdirSync(snapshotDirectory)) {
      expect(readFileSync(join(snapshotDirectory, name), "utf8")).not.toContain(canary);
    }
    let thrown: unknown;
    try {
      await registry.publish({
        action: "create",
        workspace: filesystemWorkspace("missing-secret-canary-tree"),
        baseCommit: status.head!,
      });
    } catch (error) {
      thrown = error;
    }
    expect(thrown).toMatchObject({ code: "workspace_invalid" });
    expect(String(thrown)).not.toContain(canary);
  } finally {
    if (previous === undefined) delete process.env.THT_WS_PSD_CLINICAL_EVIDENCE_SIGNED_URLS_FILE;
    else process.env.THT_WS_PSD_CLINICAL_EVIDENCE_SIGNED_URLS_FILE = previous;
  }
});