fix(cli): harden meta init scaffold and close the Java CI reactor gate

.github/workflows/conformance.yml

@@ -160,16 +160,28 @@ jobs:
           #   composes the metamodel provider set so codegen-base/om classpath SPI does not pollute it).
           mvn -pl codegen-kotlin test -Dtest='ObjectModelConformanceTest,OutputPromptConformanceTest,ValidationConformanceTest,GeneratorRegistryConformanceTest,RegistryManifestConformanceTest' -q
 
-  java-smoke-compile:
-    # The scoped `mvn -pl ... test` jobs above compile only metadata / render /
-    # codegen-spring / codegen-kotlin (+ their -am deps). Whole modules are
-    # otherwise NEVER built by CI: codegen-mustache, codegen-plantuml,
-    # maven-plugin, dynamic, core-spring, metadata-ktx, omdb-ktx,
-    # spring-boot-starter, om, omdb. A compile break in any of them ships green.
-    # A cheap reactor-wide `install -DskipTests` compiles + packages every module
-    # in the parent reactor (integration-tests* are intentionally out-of-reactor —
-    # they need Docker), so a break in the Maven plugin / Spring Boot starter /
-    # mustache/plantuml/ktx facades fails CI here.
+  java-reactor:
+    # FULL-REACTOR build AND test of the Java parent reactor (server/java).
+    #
+    # The scoped `mvn -pl ... test` jobs above run ONLY a curated `-Dtest=` subset
+    # in metadata / render / codegen-spring / codegen-kotlin (+ their -am deps).
+    # Every other reactor module's tests are otherwise NEVER run by CI — most
+    # notably the `maven-plugin` mojo tests (MetaDataGeneratorMojoTest, DocsMojoTest,
+    # MetaDataVerifyMojoTest, ...). That gap let issue #37 ship: a mojo-test fixture
+    # broke `mvn clean install` on `main` while every PR showed green, because this
+    # job used to run `install -DskipTests` (compile only, no tests).
+    #
+    # Running a full-reactor `mvn install` (tests ON) compiles, packages, AND tests
+    # every module in the parent reactor — so a red reactor can no longer slip past
+    # green PR checks. No reactor module's tests need Docker/Testcontainers (verified:
+    # the only Testcontainers suites are integration-tests* and integration-tests-kotlin,
+    # which are INTENTIONALLY out-of-reactor and gated separately by integration-tests.yml).
+    #
+    # Intentionally still OUT of this gate (documented):
+    #   - integration-tests / integration-tests-kotlin — out-of-reactor Docker/
+    #     Testcontainers persistence + api-contract corpora; gated by integration-tests.yml.
+    #   - fatjar-smoke — standalone Spring Boot fat-jar bootstrap smoke (no tests);
+    #     out-of-reactor by design, run on demand via scripts/fatjar-smoke.sh.
     needs: fixture-lint
     runs-on: ubuntu-latest
     steps:
@@ -180,8 +192,8 @@ jobs:
           distribution: 'temurin'
           java-version: '21'
           cache: maven
-      - name: Reactor-wide compile (all modules, no tests)
-        run: cd server/java && mvn -q install -DskipTests
+      - name: Full-reactor build + test (all modules, tests on)
+        run: cd server/java && mvn -q clean install
 
   completeness-gate:
     needs: [conformance, conformance-kotlin]

CHANGELOG.md

@@ -7,6 +7,22 @@ this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ## [Unreleased]
 
+### Fixed
+- **cli — `meta init` gitignore hardening:** the scaffolded
+  `.metaobjects/.gitignore` previously ignored only `.gen-state/`, so a
+  multi-target codegen config routing a target's `outDir` under
+  `.metaobjects/<target>/src/generated/` let that regenerable generated shadow
+  get committed by default. The scaffold now also ignores `*/src/generated/` and
+  re-includes the tracked artifacts (`!migrations/`, `!config.json`,
+  `!package.meta.json`) so they can never be swept up.
+- **cli — `meta init` monorepo-subdir warning:** scaffolding the agent-context
+  `.claude/skills/` into a git subdirectory means a repo-root-launched Claude
+  session won't discover the skills (discovery walks cwd + ancestors, never down
+  into subdirs). `meta init` now warns when run inside a subdir of a git repo and
+  points at `cd <repo-root> && meta init --docs-only --server <lang>`. Scaffold
+  warnings are also now surfaced on the normal init output path (previously
+  dropped).
+
 ## [0.12.5] — 2026-06-27
 
 _npm `0.12.5` (full lockstep across all 13 `@metaobjectsdev/*` publish candidates)._

server/java/codegen-kotlin/pom.xml

@@ -132,6 +132,17 @@
       <version>1.7.3</version>
       <scope>test</scope>
     </dependency>
+    <!-- KotlinM2mTraversalCompileRunTest compiles the GENERATED Exposed Table + M:N relation
+         helpers against exposed-core, resolving the jar from the local m2 repo. Declaring it
+         test-scoped here forces Maven to resolve it into ~/.m2 during this module's build, so
+         the test no longer depends on a prior build (e.g. the reactor-excluded
+         integration-tests-kotlin) having populated the local repository first. -->
+    <dependency>
+      <groupId>org.jetbrains.exposed</groupId>
+      <artifactId>exposed-core</artifactId>
+      <version>0.55.0</version>
+      <scope>test</scope>
+    </dependency>
   </dependencies>
 
   <build>

server/typescript/packages/cli/src/commands/init.ts

@@ -24,7 +24,24 @@ const META_COMMON_JSON = JSON.stringify(
   2,
 ) + "\n";
 
+// Issue #75 — a multi-target codegen config can route a target's outDir under
+// `.metaobjects/<targetName>/src/generated/`. That output is the regenerable
+// shadow (the canonical output lives at the configured outDir; re-running
+// `meta gen` recreates the shadow), so it must NOT be committed by default. We
+// ignore the per-target generated shadow with a narrow `*/src/generated/`
+// pattern, then explicitly re-include `migrations/` and `config.json` so the
+// tracked artifacts are never swept up even if a future broad pattern were added.
 const METAOBJECTS_GITIGNORE_BODY = `.gen-state/
+
+# Per-target codegen output routed under .metaobjects/<target>/ is regenerable
+# (re-run \`meta gen\`); never commit it. The canonical output is your configured
+# outDir, not this shadow.
+*/src/generated/
+
+# These ARE meant to be tracked — keep them even if a broad pattern matches.
+!migrations/
+!config.json
+!package.meta.json
 `;
 
 function buildMetaobjectsConfigBody(dialect: "sqlite" | "postgres" | "d1" = "sqlite"): string {
@@ -96,7 +113,44 @@ async function readManifest(cwd: string): Promise<Manifest | undefined> {
   try { return JSON.parse(await readFile(p, "utf8")) as Manifest; } catch { return undefined; }
 }
 
+/**
+ * Walk up from `start` looking for a `.git` directory; return the repo root, or
+ * undefined when `start` is not inside a git working tree. (`.git` can be a file
+ * in worktrees/submodules — accept either a dir or a file.)
+ */
+function findGitRoot(start: string): string | undefined {
+  let dir = start;
+  // eslint-disable-next-line no-constant-condition
+  while (true) {
+    if (existsSyncWrap(join(dir, ".git"))) return dir;
+    const parent = dirname(dir);
+    if (parent === dir) return undefined; // reached filesystem root
+    dir = parent;
+  }
+}
+
+/**
+ * Issue #77 — Claude Code discovers `.claude/skills/` only from cwd + ANCESTOR
+ * dirs + the user level; it never walks DOWN into subdirs. So scaffolding the
+ * agent-context into a monorepo subdir means a root-launched session won't load
+ * the skills (the common case). When the init dir is inside a git repo whose
+ * root is an ANCESTOR (i.e. a subdir init), warn and point the user at the repo
+ * root. The metadata/config/migrations correctly stay in the subdir regardless.
+ */
+function warnIfMonorepoSubdir(opts: InitOptions, result: InitResult): void {
+  if (opts.noSkills) return; // no skills written → nothing to warn about
+  const gitRoot = findGitRoot(opts.cwd);
+  if (gitRoot === undefined || gitRoot === opts.cwd) return; // repo root or non-git → fine
+  const lang = opts.servers && opts.servers.length > 0 ? opts.servers[0]! : "<lang>";
+  result.warnings.push(
+    "agent-context skills scaffolded into a monorepo subdir won't be discovered from a " +
+    "root-launched session (Claude Code only walks cwd + ancestors). Scaffold the context " +
+    `at the repo root instead: cd <repo-root> && meta init --docs-only --server ${lang}`,
+  );
+}
+
 async function writeAgentContext(opts: InitOptions, result: InitResult): Promise<void> {
+  warnIfMonorepoSubdir(opts, result);
   const stack = resolveStack(opts.cwd, { servers: opts.servers ?? [], clients: opts.clients ?? [] });
   let assembled = assemble({ contentRoot: resolveAgentContextRoot(), stack });
   if (opts.noSkills) assembled = assembled.filter((f) => !f.path.startsWith(".claude/skills/"));
@@ -367,6 +421,9 @@ export async function initCommand(args: string[], cwd: string): Promise<number>
         log.info("Re-run --docs-only --refresh-docs to update; --no-wire-root to skip the root CLAUDE.md @import.");
       } else {
         log.info(nextStepsBlock());
+        // Surface any scaffold warnings (e.g. the #77 monorepo-subdir agent-context
+        // discovery warning) — these are otherwise dropped on the normal init path.
+        for (const w of result.warnings) log.warn(w);
       }
     }
     return 0;

server/typescript/packages/cli/test/init.test.ts

@@ -50,6 +50,26 @@ describe("init() — happy path", () => {
     expect(ignore).toContain(".gen-state/");
   });
 
+  // Issue #75 — a multi-target codegen config can route a target's outDir under
+  // .metaobjects/<targetName>/src/generated/. That output is regenerable (re-run
+  // `meta gen` recreates it) and must NOT be committed by default. The scaffolded
+  // .gitignore must ignore the per-target shadow WITHOUT ignoring the tracked
+  // migrations/ or config.json.
+  test("scaffolded .gitignore ignores per-target generated shadow but tracks migrations/ and config.json", async () => {
+    await init({ cwd });
+    const ignore = readFileSync(join(cwd, ".metaobjects", ".gitignore"), "utf8");
+    // The per-target generated shadow pattern is present.
+    expect(ignore).toContain("*/src/generated/");
+    // migrations/ and config.json are NOT ignored (they are meant to be tracked).
+    const lines = ignore.split("\n").map((l) => l.trim());
+    expect(lines).not.toContain("migrations/");
+    expect(lines).not.toContain("migrations");
+    expect(lines).not.toContain("config.json");
+    // A negated re-include guard keeps migrations tracked even if a broad pattern
+    // were ever to match.
+    expect(ignore).toContain("!migrations/");
+  });
+
   test("does NOT create legacy .meta/ directory", async () => {
     await init({ cwd });
     expect(existsSync(join(cwd, ".meta"))).toBe(false);
@@ -134,6 +154,39 @@ describe("init() --force config preservation", () => {
   });
 });
 
+// Issue #77 — `meta init` scaffolds agent-context skills relative to cwd. In a
+// monorepo subdir the skills land where Claude Code won't discover them (it only
+// walks cwd + ancestors + user level, never down into subdirs). Detect that case
+// and WARN, pointing the user at the repo root.
+describe("init() — monorepo-subdir agent-context warning (#77)", () => {
+  test("warns when init runs from a subdir of a git repo (skills won't be discovered from root)", async () => {
+    // cwd is a temp dir; make it a git repo root, then init from a nested subdir.
+    mkdirSync(join(cwd, ".git"));
+    const subdir = join(cwd, "packages", "api");
+    mkdirSync(subdir, { recursive: true });
+
+    const result = await init({ cwd: subdir });
+    const warned = result.warnings.some(
+      (w) => /repo root/i.test(w) && /--docs-only/.test(w),
+    );
+    expect(warned).toBe(true);
+  });
+
+  test("does NOT warn when init runs at the git repo root", async () => {
+    mkdirSync(join(cwd, ".git"));
+    const result = await init({ cwd });
+    const warned = result.warnings.some((w) => /repo root/i.test(w) && /--docs-only/.test(w));
+    expect(warned).toBe(false);
+  });
+
+  test("does NOT warn when init runs in a non-git directory", async () => {
+    // cwd has no .git anywhere up the tree (tmpdir).
+    const result = await init({ cwd });
+    const warned = result.warnings.some((w) => /repo root/i.test(w) && /--docs-only/.test(w));
+    expect(warned).toBe(false);
+  });
+});
+
 describe("init --d1", () => {
   test("scaffolds config with migrate.dialect = 'd1' and prefilled binding from wrangler.toml", async () => {
     writeFileSync(join(cwd, "wrangler.toml"), [