diff --git a/CHANGELOG.md b/CHANGELOG.md
index e7b1866e..63162f75 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,17 @@ All notable changes to this project will be documented in this file.
 
 ---
 
+## [0.42.6] - 2026-03-26
+
+### Fixed
+
+- `specfact init ide` multi-source export writes prompts to a **flat** layout under the IDE export root (for example `.github/prompts/` or `.cursor/commands/`) so editors and agents can discover `specfact*.prompt.md` (or equivalent) without per-source subfolders.
+- Prompt catalog: **core** omits template basenames already provided by an installed module, avoiding duplicate exports when both ship the same filename.
+- Re-export removes legacy per-source segment directories and prunes stale flat `specfact*` exports when the selected sources change.
+- Tests: import `pytest` for `MonkeyPatch` annotations in init IDE prompt selection tests (Ruff F821).
+
+---
+
 ## [0.42.5] - 2026-03-25
 
 ### Added
diff --git a/openspec/changes/init-ide-prompt-source-selection/TDD_EVIDENCE.md b/openspec/changes/init-ide-prompt-source-selection/TDD_EVIDENCE.md
index af3baded..5ea436b2 100644
--- a/openspec/changes/init-ide-prompt-source-selection/TDD_EVIDENCE.md
+++ b/openspec/changes/init-ide-prompt-source-selection/TDD_EVIDENCE.md
@@ -10,3 +10,9 @@
 
 - Command: `hatch run pytest tests/unit/modules/init/test_init_ide_prompt_selection.py tests/unit/utils/test_ide_setup.py tests/e2e/test_init_command.py -q`
 - Status: green after `ide_setup` catalog + namespaced copy, `init ide` wiring, startup_checks rglob, and e2e path updates.
+
+## Follow-up: flat export + core/module dedupe (2026-03-26)
+
+- **Change:** Multi-source export uses a flat IDE folder; core omits template basenames covered by any module; legacy per-source subfolders are removed on export.
+- **Tests:** `hatch test tests/unit/utils/test_ide_setup.py tests/unit/modules/init/test_init_ide_prompt_selection.py -v` — all passed.
+- **Contract:** `hatch run contract-test` — PASS.
diff --git a/openspec/changes/init-ide-prompt-source-selection/specs/init-ide-prompt-source-selection/spec.md b/openspec/changes/init-ide-prompt-source-selection/specs/init-ide-prompt-source-selection/spec.md
index e1b00dc3..535a42f4 100644
--- a/openspec/changes/init-ide-prompt-source-selection/specs/init-ide-prompt-source-selection/spec.md
+++ b/openspec/changes/init-ide-prompt-source-selection/specs/init-ide-prompt-source-selection/spec.md
@@ -51,11 +51,16 @@ Non-interactive `specfact init ide` SHALL accept a comma-separated prompt source
 - **WHEN** a user passes a prompt source token that is not `all`, not `core`, and not an installed module id with prompt resources
 - **THEN** the command fails with actionable guidance describing the invalid token and the available prompt sources.
 
-### Requirement: Exported Prompt Files Must Preserve Source Provenance
+### Requirement: Exported Prompt Files Must Be IDE-Discoverable With Deterministic Single Sourcing
 
-Exported prompt files SHALL preserve module/core provenance so collisions are deterministic and later command-surface migrations do not silently overwrite unrelated prompts.
+Exported prompts for VS Code / Copilot (under ``.github/prompts/``) and other multi-source IDE targets SHALL use a **flat** layout (no per-source subfolders) so editors and agents can discover ``specfact*.prompt.md`` (or equivalent) at the export root.
 
-#### Scenario: Multiple sources expose similarly named prompts
-- **WHEN** `core` and one or more installed modules expose prompt files with overlapping basenames or command affinity
-- **THEN** the exported IDE-facing output preserves which source owns each prompt
-- **AND** the collision outcome is deterministic and visible to the user.
+#### Scenario: Core defers to modules on overlapping template basenames
+- **WHEN** `core` and one or more installed modules expose the same source filename (e.g. ``specfact.01-import.md``)
+- **THEN** the prompt catalog SHALL list that basename only under the owning module source
+- **AND** `core` SHALL NOT duplicate that basename so exports are single-sourced.
+
+#### Scenario: Multiple module sources expose the same basename
+- **WHEN** two installed modules expose the same template basename
+- **THEN** the merged export uses a deterministic last-wins rule by sorted source id (later id overwrites earlier)
+- **AND** the flat export contains exactly one file per output basename.
diff --git a/pyproject.toml b/pyproject.toml
index 3f7a2a96..d9f7f66f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "specfact-cli"
-version = "0.42.5"
+version = "0.42.6"
 description = "The swiss knife CLI for agile DevOps teams. Keep backlog, specs, tests, and code in sync with validation and contract enforcement for new projects and long-lived codebases."
 readme = "README.md"
 requires-python = ">=3.11"
diff --git a/setup.py b/setup.py
index 278e4fa8..b9cb503c 100644
--- a/setup.py
+++ b/setup.py
@@ -7,7 +7,7 @@
 if __name__ == "__main__":
     _setup = setup(
         name="specfact-cli",
-        version="0.42.5",
+        version="0.42.6",
         description=(
             "The swiss knife CLI for agile DevOps teams. Keep backlog, specs, tests, and code in sync with "
             "validation and contract enforcement for new projects and long-lived codebases."
diff --git a/src/__init__.py b/src/__init__.py
index 9f78d9d9..123f4b38 100644
--- a/src/__init__.py
+++ b/src/__init__.py
@@ -3,4 +3,4 @@
 """
 
 # Package version: keep in sync with pyproject.toml, setup.py, src/specfact_cli/__init__.py
-__version__ = "0.42.5"
+__version__ = "0.42.6"
diff --git a/src/specfact_cli/__init__.py b/src/specfact_cli/__init__.py
index 065da8ad..9d7aa16c 100644
--- a/src/specfact_cli/__init__.py
+++ b/src/specfact_cli/__init__.py
@@ -42,6 +42,6 @@ def _bootstrap_bundle_paths() -> None:
 
 _bootstrap_bundle_paths()
 
-__version__ = "0.42.5"
+__version__ = "0.42.6"
 
 __all__ = ["__version__"]
diff --git a/src/specfact_cli/modules/init/module-package.yaml b/src/specfact_cli/modules/init/module-package.yaml
index 3a9f2719..558eab8f 100644
--- a/src/specfact_cli/modules/init/module-package.yaml
+++ b/src/specfact_cli/modules/init/module-package.yaml
@@ -1,5 +1,5 @@
 name: init
-version: 0.1.17
+version: 0.1.18
 commands:
   - init
 category: core
@@ -17,5 +17,5 @@ publisher:
 description: Initialize SpecFact workspace and bootstrap local configuration.
 license: Apache-2.0
 integrity:
-  checksum: sha256:589ec7f24e7d0129cf61ad972e9f505c744ae14bd84db32cc241bc5013834163
-  signature: 9hiFgBYZZwCTMBRDBgly07v5JejhDHWXyX3/tTkTYOjjtkFT7xjZs2Pyea7l1mt2dhUZ/Tet4bdDRXyeSNcYCg==
+  checksum: sha256:218801ddd11b02e90e386a3019685add0d14a9a09d246ef958c05f53c9b46a72
+  signature: o9QdwF5+ASt8dJy5D38PgMy7pysqZUJqOaDHHjcRPXoI1dGpeSyOKjJOOtboqoH9qN2a+4nhZX6S5NGp8hlPCA==
diff --git a/src/specfact_cli/modules/init/src/commands.py b/src/specfact_cli/modules/init/src/commands.py
index 0fa41ea8..814f2ce4 100644
--- a/src/specfact_cli/modules/init/src/commands.py
+++ b/src/specfact_cli/modules/init/src/commands.py
@@ -79,7 +79,7 @@ def copy_templates_to_ide(
     *,
     prompts_by_source: dict[str, list[Path]] | None = None,
 ) -> tuple[list[Path], Path | None]:
-    """Discover prompt templates and copy them; use ``prompts_by_source`` for namespaced multi-source export."""
+    """Discover prompt templates and copy them; use ``prompts_by_source`` for multi-source flat export."""
     if prompts_by_source is not None:
         return copy_prompts_by_source_to_ide(repo_path, ide, prompts_by_source, force)
     return _copy_template_files_to_ide(repo_path, ide, discover_prompt_template_files(repo_path), force)
diff --git a/src/specfact_cli/utils/ide_setup.py b/src/specfact_cli/utils/ide_setup.py
index d4d7a6aa..60497394 100644
--- a/src/specfact_cli/utils/ide_setup.py
+++ b/src/specfact_cli/utils/ide_setup.py
@@ -195,6 +195,18 @@ def _core_prompt_template_paths(repo_path: Path, include_package_fallback: bool)
     return []
 
 
+def _core_prompts_excluding_module_basenames(
+    core_files: list[Path],
+    module_catalog: dict[str, list[Path]],
+) -> list[Path]:
+    """Drop core templates whose basename is already provided by an installed module (single source of truth)."""
+    module_basenames: set[str] = set()
+    for paths in module_catalog.values():
+        for p in paths:
+            module_basenames.add(p.name)
+    return [p for p in core_files if p.name not in module_basenames]
+
+
 def _module_prompt_sources_catalog(repo_path: Path) -> dict[str, list[Path]]:
     from specfact_cli.registry.module_packages import CORE_MODULE_ORDER, discover_package_metadata
 
@@ -249,12 +261,17 @@ def discover_prompt_sources_catalog(
 
     Core templates come from the repo checkout or the installed ``specfact_cli`` package. Module templates
     are discovered from effective module roots (builtin, project, user, marketplace, custom).
+
+    When a module ships a template with the same source filename as core (e.g. ``specfact.01-import.md``),
+    the module copy wins: core does not list that basename so exports stay single-sourced.
     """
-    catalog: dict[str, list[Path]] = {}
+    module_catalog = _module_prompt_sources_catalog(repo_path)
     core_files = _core_prompt_template_paths(repo_path, include_package_fallback)
-    if core_files:
-        catalog[PROMPT_SOURCE_CORE] = list(core_files)
-    catalog.update(_module_prompt_sources_catalog(repo_path))
+    core_filtered = _core_prompts_excluding_module_basenames(core_files, module_catalog)
+    catalog: dict[str, list[Path]] = {}
+    if core_filtered:
+        catalog[PROMPT_SOURCE_CORE] = list(core_filtered)
+    catalog.update(module_catalog)
     return catalog
 
 
@@ -378,71 +395,75 @@ def _output_filename_for_template(template_path: Path, format_type: str) -> str:
     return template_path.name
 
 
-def _safe_resolved_segment_dir(repo_path: Path, ide: str, segment: str) -> Path | None:
-    """Return ``repo_path / ide_folder / segment`` resolved, or ``None`` if it escapes the IDE export root."""
-    config = IDE_CONFIG[ide]
-    base = (repo_path / str(config["folder"])).resolve()
-    segment_dir = (base / segment).resolve()
-    try:
-        segment_dir.relative_to(base)
-    except ValueError:
-        return None
-    return segment_dir
+def _merge_prompt_export_outputs_by_basename(
+    prompts_by_source: dict[str, list[Path]],
+    format_type: str,
+) -> dict[str, Path]:
+    """Map IDE output filename to source template; later sources win over core on basename collisions."""
+    ordered = sorted(
+        prompts_by_source.items(),
+        key=lambda item: (item[0] != PROMPT_SOURCE_CORE, item[0]),
+    )
+    out: dict[str, Path] = {}
+    for _source_id, paths in ordered:
+        for p in paths:
+            out[_output_filename_for_template(p, format_type)] = p
+    return out
 
 
-def _prune_segment_exports_not_in_expected(
-    repo_path: Path,
-    ide: str,
-    segment: str,
-    template_paths: list[Path],
-) -> None:
-    """Remove files under ``ide_folder/segment`` that are not part of this export (same filenames as copy)."""
-    if not template_paths:
-        return
+def _cleanup_legacy_multisource_segment_dirs(repo_path: Path, ide: str) -> None:
+    """Remove per-source subfolders from older multi-source exports (layout is now flat under the IDE root)."""
     config = IDE_CONFIG[ide]
-    format_type = str(config["format"])
-    segment_dir = _safe_resolved_segment_dir(repo_path, ide, segment)
-    if segment_dir is None or not segment_dir.is_dir():
+    base = (repo_path / str(config["folder"])).resolve()
+    if not base.is_dir():
         return
-    expected_resolved: set[Path] = {
-        (segment_dir / _output_filename_for_template(tp, format_type)).resolve() for tp in template_paths
-    }
-    for p in list(segment_dir.iterdir()):
-        if not p.is_file():
+    for child in list(base.iterdir()):
+        if not child.is_dir():
             continue
-        if p.resolve() not in expected_resolved:
-            try:
-                p.unlink()
-                console.print(f"[dim]Removed stale prompt export:[/dim] {p}")
-            except OSError as exc:
-                console.print(f"[yellow]Could not remove stale export {p}:[/yellow] {exc}")
+        if child.name != PROMPT_SOURCE_CORE and "__" not in child.name:
+            continue
+        try:
+            child.resolve().relative_to(base)
+        except ValueError:
+            continue
+        try:
+            shutil.rmtree(child)
+            console.print(f"[dim]Removed legacy prompt export segment:[/dim] {child}")
+        except OSError as exc:
+            console.print(f"[yellow]Could not remove legacy segment {child}:[/yellow] {exc}")
+
+
+def _flat_export_glob_pattern_for_prune(format_type: str) -> str:
+    """Glob for SpecFact-managed flat exports; must stay aligned with ``_output_filename_for_template``."""
+    if format_type == "prompt.md":
+        return "specfact*.prompt.md"
+    if format_type == "toml":
+        return "specfact*.toml"
+    return "specfact*.md"
 
 
-def _remove_unselected_prompt_export_segments(
+def _prune_flat_specfact_exports_not_in_expected(
     repo_path: Path,
     ide: str,
-    prompts_by_source: dict[str, list[Path]],
+    expected_output_names: set[str],
 ) -> None:
-    """Remove on-disk segment directories under the IDE export root that are not in this selective export."""
+    """Remove prior flat ``specfact*`` exports that are not part of this merged export."""
     config = IDE_CONFIG[ide]
+    format_type = str(config["format"])
     base = (repo_path / str(config["folder"])).resolve()
-    selected_segments = {source_id_to_path_segment(sid) for sid in prompts_by_source}
     if not base.is_dir():
         return
-    for child in list(base.iterdir()):
-        if not child.is_dir():
-            continue
-        try:
-            child.resolve().relative_to(base)
-        except ValueError:
+    pattern = _flat_export_glob_pattern_for_prune(format_type)
+    for p in base.glob(pattern):
+        if not p.is_file():
             continue
-        if child.name in selected_segments:
+        if p.name in expected_output_names:
             continue
         try:
-            shutil.rmtree(child)
-            console.print(f"[dim]Removed unselected export segment:[/dim] {child}")
+            p.unlink()
+            console.print(f"[dim]Removed stale prompt export:[/dim] {p}")
         except OSError as exc:
-            console.print(f"[yellow]Could not remove segment {child}:[/yellow] {exc}")
+            console.print(f"[yellow]Could not remove stale export {p}:[/yellow] {exc}")
 
 
 def _copy_template_files_to_ide(
@@ -507,7 +528,7 @@ def expected_ide_prompt_export_paths(
     *,
     prompt_source_ids: frozenset[str] | None = None,
 ) -> list[Path]:
-    """Return expected on-disk paths for exported IDE prompts (source-namespaced layout).
+    """Return expected on-disk paths for exported IDE prompts (flat layout under the IDE export folder).
 
     If ``prompt_source_ids`` is set (from ``.specfact/ide-prompt-export.yaml``), only those sources are
     expected—matching a selective ``init ide --prompts`` run. Otherwise the full discovered catalog is used.
@@ -518,12 +539,8 @@ def expected_ide_prompt_export_paths(
     catalog = discover_prompt_sources_catalog(repo_path)
     if prompt_source_ids is not None:
         catalog = {k: v for k, v in catalog.items() if k in prompt_source_ids}
-    paths: list[Path] = []
-    for sid, templates in sorted(catalog.items(), key=lambda item: (item[0] != PROMPT_SOURCE_CORE, item[0])):
-        segment = source_id_to_path_segment(sid)
-        for template_path in templates:
-            paths.append(base / segment / _output_filename_for_template(template_path, format_type))
-    return paths
+    merged = _merge_prompt_export_outputs_by_basename(catalog, format_type)
+    return [base / name for name in sorted(merged.keys())]
 
 
 @beartype
@@ -551,13 +568,12 @@ def count_outdated_ide_prompt_exports(
     catalog = discover_prompt_sources_catalog(repo_path)
     if prompt_source_ids is not None:
         catalog = {k: v for k, v in catalog.items() if k in prompt_source_ids}
+    merged = _merge_prompt_export_outputs_by_basename(catalog, format_type)
     outdated = 0
-    for sid, paths in catalog.items():
-        segment = source_id_to_path_segment(sid)
-        for src in paths:
-            dest = base / segment / _output_filename_for_template(src, format_type)
-            if src.exists() and dest.exists() and dest.stat().st_mtime < src.stat().st_mtime:
-                outdated += 1
+    for dest_name, src in merged.items():
+        dest = base / dest_name
+        if src.exists() and dest.exists() and dest.stat().st_mtime < src.stat().st_mtime:
+            outdated += 1
     return outdated
 
 
@@ -581,25 +597,18 @@ def copy_prompts_by_source_to_ide(
     prompts_by_source: dict[str, list[Path]],
     force: bool = False,
 ) -> tuple[list[Path], Path | None]:
-    """Copy prompts grouped by source id into source-namespaced subfolders under the IDE export directory."""
-    all_copied: list[Path] = []
-    _remove_unselected_prompt_export_segments(repo_path, ide, prompts_by_source)
-    ordered = sorted(
-        prompts_by_source.items(),
-        key=lambda item: (item[0] != PROMPT_SOURCE_CORE, item[0]),
+    """Copy prompts from multiple sources into a single flat folder under the IDE export directory."""
+    config = IDE_CONFIG[ide]
+    format_type = str(config["format"])
+    _cleanup_legacy_multisource_segment_dirs(repo_path, ide)
+    merged = _merge_prompt_export_outputs_by_basename(prompts_by_source, format_type)
+    _prune_flat_specfact_exports_not_in_expected(repo_path, ide, set(merged.keys()))
+    template_list = list(merged.values())
+    all_copied, _settings = _copy_template_files_to_ide(
+        repo_path, ide, template_list, force, source_segment=None, write_settings=False
     )
-    for source_id, paths in ordered:
-        if not paths:
-            continue
-        segment = source_id_to_path_segment(source_id)
-        _prune_segment_exports_not_in_expected(repo_path, ide, segment, paths)
-        copied, _settings = _copy_template_files_to_ide(
-            repo_path, ide, paths, force, source_segment=segment, write_settings=False
-        )
-        all_copied.extend(copied)
 
     settings_path: Path | None = None
-    config = IDE_CONFIG[ide]
     settings_file = config.get("settings_file")
     if settings_file and isinstance(settings_file, str):
         settings_path = create_vscode_settings(repo_path, settings_file, prompts_by_source=prompts_by_source)
@@ -764,27 +773,16 @@ def copy_templates_to_ide(
 
 
 def _vscode_prompt_recommendation_paths_from_sources(prompts_by_source: dict[str, list[Path]]) -> list[str]:
-    """Build `.github/prompts/...` recommendation strings matching namespaced IDE export layout."""
-    prompt_files: list[str] = []
-    for source_id, paths in sorted(
-        prompts_by_source.items(),
-        key=lambda item: (item[0] != PROMPT_SOURCE_CORE, item[0]),
-    ):
-        segment = source_id_to_path_segment(source_id)
-        for template_path in paths:
-            prompt_files.append(f".github/prompts/{segment}/{template_path.stem}.prompt.md")
-    return prompt_files
+    """Build `.github/prompts/...` recommendation strings matching flat IDE export layout."""
+    merged = _merge_prompt_export_outputs_by_basename(prompts_by_source, "prompt.md")
+    return [f".github/prompts/{name}" for name in sorted(merged.keys())]
 
 
 def _vscode_prompt_paths_from_full_catalog(repo_path: Path) -> list[str]:
-    """Recommendation paths for the full discovered prompt catalog (namespaced segments)."""
+    """Recommendation paths for the full discovered prompt catalog (flat under ``.github/prompts/``)."""
     catalog = discover_prompt_sources_catalog(repo_path)
-    out: list[str] = []
-    for source_id, paths in sorted(catalog.items(), key=lambda item: (item[0] != PROMPT_SOURCE_CORE, item[0])):
-        segment = source_id_to_path_segment(source_id)
-        for template_path in paths:
-            out.append(f".github/prompts/{segment}/{template_path.stem}.prompt.md")
-    return out
+    merged = _merge_prompt_export_outputs_by_basename(catalog, "prompt.md")
+    return [f".github/prompts/{name}" for name in sorted(merged.keys())]
 
 
 def _finalize_vscode_prompt_recommendation_paths(repo_path: Path, prompt_files: list[str]) -> list[str]:
@@ -883,7 +881,7 @@ def create_vscode_settings(
         prompts_by_source: When set (e.g. from ``copy_prompts_by_source_to_ide``), recommendations list only
             templates from that export; prior **SpecFact-managed** ``.github/prompts/`` entries (paths whose
             filename looks like ``specfact*.prompt.md``) are removed so selective ``--prompts`` runs do not
-            leave stale exports; other ``.github/prompts/`` entries and paths outside that folder are preserved.
+            leave stale recommendations; other ``.github/prompts/`` entries and paths outside that folder are preserved.
             When ``None``,
             recommendations follow the full discovered catalog (or legacy flat fallbacks).
 
diff --git a/tests/e2e/test_init_command.py b/tests/e2e/test_init_command.py
index 11d47d5a..0c229a2f 100644
--- a/tests/e2e/test_init_command.py
+++ b/tests/e2e/test_init_command.py
@@ -2,6 +2,7 @@
 
 import os
 
+import pytest
 from typer.testing import CliRunner
 
 from specfact_cli.cli import app
@@ -10,6 +11,14 @@
 runner = CliRunner()
 
 
+@pytest.fixture(autouse=True)
+def _isolate_user_prompt_modules_for_init_e2e(monkeypatch: pytest.MonkeyPatch) -> None:
+    """Do not pick up ~/.specfact/modules prompt bundles; tests use repo ``resources/prompts`` only."""
+    import specfact_cli.utils.ide_setup as ide_setup_module
+
+    monkeypatch.setattr(ide_setup_module, "_module_prompt_sources_catalog", lambda _rp: {})
+
+
 class TestInitCommandE2E:
     """End-to-end tests for specfact init command."""
 
@@ -40,8 +49,8 @@ def test_init_auto_detect_cursor(self, tmp_path, monkeypatch):
         assert "Cursor" in result.stdout
         assert ".cursor/commands/" in result.stdout
 
-        # Verify templates were copied (namespaced by source: core/)
-        cursor_dir = tmp_path / ".cursor" / "commands" / "core"
+        # Verify templates were copied (flat layout under the IDE export root)
+        cursor_dir = tmp_path / ".cursor" / "commands"
         assert cursor_dir.exists()
         assert (cursor_dir / "specfact.01-import.md").exists()
         assert (cursor_dir / "specfact.02-plan.md").exists()
@@ -64,8 +73,8 @@ def test_init_explicit_cursor(self, tmp_path):
         assert "Cursor" in result.stdout
         assert ".cursor/commands/" in result.stdout
 
-        # Verify template was copied (namespaced: core/)
-        cursor_dir = tmp_path / ".cursor" / "commands" / "core"
+        # Verify template was copied (flat layout)
+        cursor_dir = tmp_path / ".cursor" / "commands"
         assert cursor_dir.exists()
         assert (cursor_dir / "specfact.01-import.md").exists()
 
@@ -87,8 +96,8 @@ def test_init_explicit_vscode(self, tmp_path):
         assert "VS Code" in result.stdout
         assert ".github/prompts/" in result.stdout
 
-        # Verify template was copied (namespaced: core/)
-        prompts_dir = tmp_path / ".github" / "prompts" / "core"
+        # Verify template was copied (flat layout)
+        prompts_dir = tmp_path / ".github" / "prompts"
         assert prompts_dir.exists()
         assert (prompts_dir / "specfact.01-import.prompt.md").exists()
 
@@ -114,8 +123,8 @@ def test_init_explicit_copilot(self, tmp_path):
         assert "GitHub Copilot" in result.stdout
         assert ".github/prompts/" in result.stdout
 
-        # Verify template was copied (namespaced: core/)
-        prompts_dir = tmp_path / ".github" / "prompts" / "core"
+        # Verify template was copied (flat layout)
+        prompts_dir = tmp_path / ".github" / "prompts"
         assert prompts_dir.exists()
         assert (prompts_dir / "specfact.01-import.prompt.md").exists()
 
@@ -127,8 +136,8 @@ def test_init_skips_existing_files_without_force(self, tmp_path):
         (templates_dir / "specfact.01-import.md").write_text("---\ndescription: Analyze\n---\nContent")
         (templates_dir / "specfact.02-plan.md").write_text("---\ndescription: Plan Init\n---\nContent")
 
-        # Pre-create one exported file (namespaced: core/) but not all
-        cursor_dir = tmp_path / ".cursor" / "commands" / "core"
+        # Pre-create one exported file (flat path) but not all
+        cursor_dir = tmp_path / ".cursor" / "commands"
         cursor_dir.mkdir(parents=True)
         (cursor_dir / "specfact.01-import.md").write_text("existing content")
 
@@ -156,8 +165,8 @@ def test_init_overwrites_with_force(self, tmp_path):
         templates_dir.mkdir(parents=True)
         (templates_dir / "specfact.01-import.md").write_text("---\ndescription: Analyze\n---\nNew content")
 
-        # Pre-create one file under the namespaced core/ export path
-        cursor_dir = tmp_path / ".cursor" / "commands" / "core"
+        # Pre-create one file under the flat export path
+        cursor_dir = tmp_path / ".cursor" / "commands"
         cursor_dir.mkdir(parents=True)
         (cursor_dir / "specfact.01-import.md").write_text("existing content")
 
@@ -246,8 +255,8 @@ def test_init_auto_detect_vscode(self, tmp_path, monkeypatch):
         assert "VS Code" in result.stdout or "vscode" in result.stdout.lower()
         assert ".github/prompts/" in result.stdout
 
-        # Verify templates were copied (namespaced: core/)
-        prompts_dir = tmp_path / ".github" / "prompts" / "core"
+        # Verify templates were copied (flat layout)
+        prompts_dir = tmp_path / ".github" / "prompts"
         assert prompts_dir.exists()
         assert (prompts_dir / "specfact.01-import.prompt.md").exists()
 
@@ -279,8 +288,8 @@ def test_init_auto_detect_claude(self, tmp_path, monkeypatch):
         assert result.exit_code == 0
         assert "Claude Code" in result.stdout or "claude" in result.stdout.lower()
 
-        # Verify templates were copied (namespaced: core/)
-        claude_dir = tmp_path / ".claude" / "commands" / "core"
+        # Verify templates were copied (flat layout)
+        claude_dir = tmp_path / ".claude" / "commands"
         assert claude_dir.exists()
         assert (claude_dir / "specfact.01-import.md").exists()
 
diff --git a/tests/unit/modules/init/test_init_ide_prompt_selection.py b/tests/unit/modules/init/test_init_ide_prompt_selection.py
index 4c4ff4fe..fe81b7c7 100644
--- a/tests/unit/modules/init/test_init_ide_prompt_selection.py
+++ b/tests/unit/modules/init/test_init_ide_prompt_selection.py
@@ -4,6 +4,7 @@
 
 from pathlib import Path
 
+import pytest
 from typer.testing import CliRunner
 
 from specfact_cli.cli import app
@@ -21,7 +22,13 @@ def test_source_id_to_path_segment_sanitizes_slashes() -> None:
     assert source_id_to_path_segment("core") == "core"
 
 
-def test_discover_prompt_sources_catalog_includes_core_from_repo(tmp_path: Path) -> None:
+def test_discover_prompt_sources_catalog_includes_core_from_repo(
+    tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+) -> None:
+    import specfact_cli.utils.ide_setup as ide_setup_module
+
+    monkeypatch.setattr(ide_setup_module, "_module_prompt_sources_catalog", lambda _rp: {})
+
     prompts = tmp_path / "resources" / "prompts"
     prompts.mkdir(parents=True)
     p1 = prompts / "specfact.01-import.md"
@@ -33,7 +40,31 @@ def test_discover_prompt_sources_catalog_includes_core_from_repo(tmp_path: Path)
     assert p1 in catalog[PROMPT_SOURCE_CORE]
 
 
-def test_copy_prompts_by_source_to_ide_namespaces_by_source(tmp_path: Path) -> None:
+def test_discover_prompt_sources_catalog_omits_core_when_module_has_same_basename(tmp_path: Path) -> None:
+    core = tmp_path / "resources" / "prompts"
+    core.mkdir(parents=True)
+    p_core = core / "specfact.01-import.md"
+    p_core.write_text("---\n---\n# core\n", encoding="utf-8")
+
+    package_dir = tmp_path / ".specfact" / "modules" / "specfact-codebase"
+    prompt_dir = package_dir / "resources" / "prompts"
+    prompt_dir.mkdir(parents=True)
+    (package_dir / "module-package.yaml").write_text(
+        "name: nold-ai/specfact-codebase\nversion: '0.1.0'\ncommands: [codebase]\ncategory: codebase\n"
+        "bundle_group_command: code\n",
+        encoding="utf-8",
+    )
+    p_mod = prompt_dir / "specfact.01-import.md"
+    p_mod.write_text("---\n---\n# mod\n", encoding="utf-8")
+
+    catalog = discover_prompt_sources_catalog(tmp_path, include_package_fallback=False)
+
+    assert PROMPT_SOURCE_CORE not in catalog
+    assert "nold-ai/specfact-codebase" in catalog
+    assert p_mod in catalog["nold-ai/specfact-codebase"]
+
+
+def test_copy_prompts_by_source_to_ide_exports_flat_under_ide_root(tmp_path: Path) -> None:
     prompts = tmp_path / "resources" / "prompts"
     prompts.mkdir(parents=True)
     f1 = prompts / "specfact.01-import.md"
@@ -47,11 +78,13 @@ def test_copy_prompts_by_source_to_ide_namespaces_by_source(tmp_path: Path) -> N
     by_source = {PROMPT_SOURCE_CORE: [f1], "nold-ai/specfact-backlog": [f2]}
     copied, _settings = copy_prompts_by_source_to_ide(tmp_path, "cursor", by_source, force=True)
 
-    assert (tmp_path / ".cursor" / "commands" / "core" / "specfact.01-import.md") in copied
-    assert (tmp_path / ".cursor" / "commands" / "nold-ai__specfact-backlog" / "specfact.backlog-add.md") in copied
+    cmd = tmp_path / ".cursor" / "commands"
+    assert (cmd / "specfact.01-import.md") in copied
+    assert (cmd / "specfact.backlog-add.md") in copied
+    assert not (cmd / "core").exists()
 
 
-def test_copy_prompts_by_source_to_ide_prunes_stale_in_selected_segment(tmp_path: Path) -> None:
+def test_copy_prompts_by_source_to_ide_prunes_stale_in_flat_export(tmp_path: Path) -> None:
     """Re-exporting a subset of core templates removes outputs that are no longer expected."""
     prompts = tmp_path / "resources" / "prompts"
     prompts.mkdir(parents=True)
@@ -60,18 +93,18 @@ def test_copy_prompts_by_source_to_ide_prunes_stale_in_selected_segment(tmp_path
     f2 = prompts / "specfact.02-plan.md"
     f2.write_text("---\ndescription: B\n---\n# B\n", encoding="utf-8")
 
-    core_dir = tmp_path / ".cursor" / "commands" / "core"
+    cmd_dir = tmp_path / ".cursor" / "commands"
     copy_prompts_by_source_to_ide(tmp_path, "cursor", {PROMPT_SOURCE_CORE: [f1, f2]}, force=True)
-    assert (core_dir / "specfact.01-import.md").is_file()
-    assert (core_dir / "specfact.02-plan.md").is_file()
+    assert (cmd_dir / "specfact.01-import.md").is_file()
+    assert (cmd_dir / "specfact.02-plan.md").is_file()
 
     copy_prompts_by_source_to_ide(tmp_path, "cursor", {PROMPT_SOURCE_CORE: [f1]}, force=True)
-    assert (core_dir / "specfact.01-import.md").is_file()
-    assert not (core_dir / "specfact.02-plan.md").exists()
+    assert (cmd_dir / "specfact.01-import.md").is_file()
+    assert not (cmd_dir / "specfact.02-plan.md").exists()
 
 
-def test_copy_prompts_by_source_to_ide_removes_unselected_catalog_segment(tmp_path: Path) -> None:
-    """Selective export removes IDE segment dirs for catalog sources not in this run."""
+def test_copy_prompts_by_source_to_ide_removes_unselected_module_exports_from_flat(tmp_path: Path) -> None:
+    """Selective export removes flat outputs from catalog sources not in this run."""
     prompts = tmp_path / "resources" / "prompts"
     prompts.mkdir(parents=True)
     f1 = prompts / "specfact.01-import.md"
@@ -88,18 +121,18 @@ def test_copy_prompts_by_source_to_ide_removes_unselected_catalog_segment(tmp_pa
     f2 = prompt_dir / "specfact.backlog-add.md"
     f2.write_text("---\ndescription: B\n---\n# B\n", encoding="utf-8")
 
-    mod_seg = tmp_path / ".cursor" / "commands" / "nold-ai__specfact-backlog"
+    cmd_dir = tmp_path / ".cursor" / "commands"
     copy_prompts_by_source_to_ide(
         tmp_path,
         "cursor",
         {PROMPT_SOURCE_CORE: [f1], "nold-ai/specfact-backlog": [f2]},
         force=True,
     )
-    assert (mod_seg / "specfact.backlog-add.md").is_file()
+    assert (cmd_dir / "specfact.backlog-add.md").is_file()
 
     copy_prompts_by_source_to_ide(tmp_path, "cursor", {PROMPT_SOURCE_CORE: [f1]}, force=True)
-    assert not mod_seg.exists()
-    assert (tmp_path / ".cursor" / "commands" / "core" / "specfact.01-import.md").is_file()
+    assert (cmd_dir / "specfact.01-import.md").is_file()
+    assert not (cmd_dir / "specfact.backlog-add.md").exists()
 
 
 def test_parse_prompts_option_all_expands_to_full_catalog() -> None:
diff --git a/tests/unit/specfact_cli/registry/test_init_module_lifecycle_ux.py b/tests/unit/specfact_cli/registry/test_init_module_lifecycle_ux.py
index b27a1780..1d4e4992 100644
--- a/tests/unit/specfact_cli/registry/test_init_module_lifecycle_ux.py
+++ b/tests/unit/specfact_cli/registry/test_init_module_lifecycle_ux.py
@@ -128,6 +128,11 @@ def test_resolve_templates_dir_uses_package_fallback_when_repo_templates_missing
     fallback_templates.mkdir(parents=True)
     monkeypatch.setattr(init_commands, "find_package_resources_path", lambda *_args: fallback_templates)
     monkeypatch.setattr("importlib.resources.files", lambda *_args: (_ for _ in ()).throw(RuntimeError("boom")))
+    monkeypatch.setattr(
+        init_commands,
+        "discover_prompt_template_files",
+        lambda repo_path, include_package_fallback=False: [],
+    )
 
     resolved = init_commands._resolve_templates_dir(tmp_path)
 
diff --git a/tests/unit/utils/test_ide_setup.py b/tests/unit/utils/test_ide_setup.py
index c6a7402e..e1fd9146 100644
--- a/tests/unit/utils/test_ide_setup.py
+++ b/tests/unit/utils/test_ide_setup.py
@@ -10,6 +10,7 @@
 from specfact_cli.utils.ide_setup import (
     PROMPT_SOURCE_CORE,
     SPECFACT_COMMANDS,
+    _flat_export_glob_pattern_for_prune,
     _is_specfact_github_prompt_path,
     copy_templates_to_ide,
     create_vscode_settings,
@@ -240,8 +241,14 @@ def test_copy_templates_copies_non_core_prompt_ids_when_discovered(self, tmp_pat
         assert (tmp_path / ".cursor" / "commands" / "specfact.backlog-add.md").exists()
 
 
-def test_discover_prompt_template_files_falls_back_to_repo_resources(tmp_path: Path) -> None:
+def test_discover_prompt_template_files_falls_back_to_repo_resources(
+    tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+) -> None:
     """Prompt discovery falls back to repo-local resources when no installed module resources exist."""
+    import specfact_cli.utils.ide_setup as ide_setup_module
+
+    monkeypatch.setattr(ide_setup_module, "_module_prompt_sources_catalog", lambda _rp: {})
+
     templates_dir = tmp_path / "resources" / "prompts"
     templates_dir.mkdir(parents=True)
     prompt_file = templates_dir / "specfact.01-import.md"
@@ -310,6 +317,13 @@ def test_discover_prompt_template_files_deduplicates_prompt_ids_by_filename(
     assert discovered == [first_prompt]
 
 
+def test_flat_export_glob_pattern_for_prune_matches_output_formats() -> None:
+    """Prune globs must align with ``_output_filename_for_template`` (including Gemini/Qwen ``*.toml``)."""
+    assert _flat_export_glob_pattern_for_prune("prompt.md") == "specfact*.prompt.md"
+    assert _flat_export_glob_pattern_for_prune("toml") == "specfact*.toml"
+    assert _flat_export_glob_pattern_for_prune("md") == "specfact*.md"
+
+
 def test_is_specfact_github_prompt_path_only_specfact_named_prompts() -> None:
     """Strip targets only ``specfact*.prompt.md`` under ``.github/prompts/`` (after path normalization)."""
     assert _is_specfact_github_prompt_path(".github/prompts/core/specfact.01-import.prompt.md")
@@ -352,7 +366,7 @@ def test_create_vscode_settings_selective_export_replaces_stale_github_prompt_pa
     assert ".github/prompts/nold-ai__mod/specfact.extra.prompt.md" not in recs
     assert ".github/prompts/custom/team-owned.prompt.md" in recs
     assert ".other/custom.prompt.md" in recs
-    assert ".github/prompts/core/specfact.01-import.prompt.md" in recs
+    assert ".github/prompts/specfact.01-import.prompt.md" in recs
 
 
 def test_specfact_commands_excludes_backlog_prompt_ids() -> None:
@@ -396,4 +410,5 @@ def test_expected_ide_prompt_export_paths_respects_prompt_source_subset(
     )
     assert len(full_paths) == 2
     assert len(subset_paths) == 1
-    assert "core" in subset_paths[0].parts
+    assert subset_paths[0].name == "c.md"
+    assert "core" not in subset_paths[0].parts