fix(integrations): stop frontmatter injection gluing onto a missing trailing newline (#4570)

* fix(integrations): stop frontmatter injection gluing onto a missing trailing newline

ClaudeIntegration/VibeIntegration/AlquimiaAIIntegration's
_inject_frontmatter_flag() detected the closing "---" line's existing
EOL and reused it when injecting a new key -- so when that "---" was
the file's last line with no trailing newline, the injected text was
appended with no newline at all, producing "user-invocable: true---"
instead of a properly separated line. This corrupts the frontmatter
(the closing delimiter is no longer alone on its own line) and, since
post_process_skill_content() chains multiple injection calls, silently
drops every subsequent key: a second call's pre-scan can no longer find
a second "---" line to inject before, so e.g.
"disable-model-invocation: false" is never added at all.

post_process_skill_content() runs on content from "external skill
generators (presets, extensions)" per its own docstring, so a trailing
newline after the closing delimiter isn't guaranteed.

DroidIntegration's own copy of this helper already emits an
unconditional "\n" instead of detecting/reusing the existing EOL,
exactly avoiding this bug -- ported that fix to the other three
implementations. Added a regression test to each of the three affected
integrations' test files, covering both the single-call corruption and
the chained-calls silent-drop.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01U74yBbvVQCPwB7Ed8Dzeu6

* fix(integrations): preserve existing EOL when injecting frontmatter flags

Per Copilot review on PR #4570: unconditionally emitting "\n" after the
injected key regressed CRLF-authored skills into mixed line endings.
Detect the closing delimiter's existing EOL (\r\n or \n) and only fall
back to "\n" when the delimiter has none at all (the original
no-trailing-newline corruption bug).

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

---------

Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com>

Author: Noor-ul-ain001

src/specify_cli/integrations/alquimia/__init__.py

@@ -152,7 +152,13 @@ def _inject_frontmatter_flag(content: str, key: str, value: str = "true") -> str
             if dash_count == 1 and stripped.startswith(f"{key}:"):
                 return content
 
-        # Inject before the closing --- of frontmatter
+        # Inject before the closing --- of frontmatter. Preserve the
+        # existing EOL style, but default to "\n" (rather than "") when the
+        # closing delimiter is the last line of the file with no trailing
+        # newline -- otherwise the injected text glues onto the "---"
+        # (e.g. "user-invocable: true---"), destroying the delimiter so a
+        # later call's pre-scan/injection never finds a second "---" and
+        # silently drops that key entirely.
         out: list[str] = []
         dash_count = 0
         injected = False
@@ -166,7 +172,7 @@ def _inject_frontmatter_flag(content: str, key: str, value: str = "true") -> str
                     elif line.endswith("\n"):
                         eol = "\n"
                     else:
-                        eol = ""
+                        eol = "\n"
                     out.append(f"{key}: {value}{eol}")
                     injected = True
             out.append(line)

src/specify_cli/integrations/claude/__init__.py

@@ -173,7 +173,13 @@ def _inject_frontmatter_flag(content: str, key: str, value: str = "true") -> str
             if dash_count == 1 and stripped.startswith(f"{key}:"):
                 return content
 
-        # Inject before the closing --- of frontmatter
+        # Inject before the closing --- of frontmatter. Preserve the
+        # existing EOL style, but default to "\n" (rather than "") when the
+        # closing delimiter is the last line of the file with no trailing
+        # newline -- otherwise the injected text glues onto the "---"
+        # (e.g. "user-invocable: true---"), destroying the delimiter so a
+        # later call's pre-scan/injection never finds a second "---" and
+        # silently drops that key entirely.
         out: list[str] = []
         dash_count = 0
         injected = False
@@ -187,7 +193,7 @@ def _inject_frontmatter_flag(content: str, key: str, value: str = "true") -> str
                     elif line.endswith("\n"):
                         eol = "\n"
                     else:
-                        eol = ""
+                        eol = "\n"
                     out.append(f"{key}: {value}{eol}")
                     injected = True
             out.append(line)

src/specify_cli/integrations/vibe/__init__.py

@@ -115,7 +115,13 @@ def _inject_frontmatter_flag(content: str, key: str, value: str = "true") -> str
             if dash_count == 1 and stripped.startswith(f"{key}:"):
                 return content
 
-        # Inject before the closing --- of frontmatter
+        # Inject before the closing --- of frontmatter. Preserve the
+        # existing EOL style, but default to "\n" (rather than "") when the
+        # closing delimiter is the last line of the file with no trailing
+        # newline -- otherwise the injected text glues onto the "---"
+        # (e.g. "user-invocable: true---"), destroying the delimiter so a
+        # later call's pre-scan/injection never finds a second "---" and
+        # silently drops that key entirely.
         out: list[str] = []
         dash_count = 0
         injected = False
@@ -129,7 +135,7 @@ def _inject_frontmatter_flag(content: str, key: str, value: str = "true") -> str
                     elif line.endswith("\n"):
                         eol = "\n"
                     else:
-                        eol = ""
+                        eol = "\n"
                     out.append(f"{key}: {value}{eol}")
                     injected = True
             out.append(line)

tests/integrations/test_integration_alquimia.py

@@ -621,6 +621,56 @@ def test_skills_default_post_process_preserves_content_without_hooks(
         assert agy.post_process_skill_content(content) == content
 
 
+class TestAlquimiaInjectFrontmatterFlagNoTrailingNewline:
+    """`_inject_frontmatter_flag` must not corrupt content whose closing
+    frontmatter delimiter is the file's last line with no trailing newline.
+
+    `post_process_skill_content` calls this helper on content from
+    "external skill generators (presets, extensions)" (per the base
+    class's docstring) -- not guaranteed to end with a trailing newline.
+    Without a newline after the injected line, the injected text glues
+    onto the closing `---`, destroying the delimiter.
+    """
+
+    def test_single_call_keeps_delimiter_on_its_own_line(self):
+        from specify_cli.integrations.alquimia import AlquimiaAIIntegration
+
+        content = "---\nname: x\n---"
+        result = AlquimiaAIIntegration._inject_frontmatter_flag(
+            content, "user-invocable"
+        )
+        assert result == "---\nname: x\nuser-invocable: true\n---"
+
+    def test_chained_calls_both_apply(self):
+        """The exact sequence `post_process_skill_content` runs: a second
+        injected key must still land, not be silently dropped because the
+        first call already destroyed the closing `---` line."""
+        from specify_cli.integrations.alquimia import AlquimiaAIIntegration
+
+        content = "---\nname: x\n---"
+        result = AlquimiaAIIntegration._inject_frontmatter_flag(
+            content, "user-invocable"
+        )
+        result = AlquimiaAIIntegration._inject_frontmatter_flag(
+            result, "disable-model-invocation", "false"
+        )
+        assert result == (
+            "---\nname: x\nuser-invocable: true\n"
+            "disable-model-invocation: false\n---"
+        )
+
+    def test_preserves_crlf_line_endings(self):
+        """When the closing delimiter *does* end with \\r\\n, the injected
+        line must reuse that EOL rather than switching the file to LF."""
+        from specify_cli.integrations.alquimia import AlquimiaAIIntegration
+
+        content = "---\r\nname: x\r\n---\r\n"
+        result = AlquimiaAIIntegration._inject_frontmatter_flag(
+            content, "user-invocable"
+        )
+        assert result == "---\r\nname: x\r\nuser-invocable: true\r\n---\r\n"
+
+
 class TestAlquimiaHookCommandNote:
     """Verify dot-to-hyphen normalization note is injected in hook sections."""
 

tests/integrations/test_integration_claude.py

@@ -591,6 +591,56 @@ def test_skills_default_post_process_preserves_content_without_hooks(self, tmp_p
         assert agy.post_process_skill_content(content) == content
 
 
+class TestClaudeInjectFrontmatterFlagNoTrailingNewline:
+    """`_inject_frontmatter_flag` must not corrupt content whose closing
+    frontmatter delimiter is the file's last line with no trailing newline.
+
+    `post_process_skill_content` calls this helper on content from
+    "external skill generators (presets, extensions)" (per its own
+    docstring) -- not guaranteed to end with a trailing newline. Without a
+    newline after the injected line, the injected text glues onto the
+    closing `---`, destroying the delimiter.
+    """
+
+    def test_single_call_keeps_delimiter_on_its_own_line(self):
+        from specify_cli.integrations.claude import ClaudeIntegration
+
+        content = "---\nname: x\n---"
+        result = ClaudeIntegration._inject_frontmatter_flag(
+            content, "user-invocable"
+        )
+        assert result == "---\nname: x\nuser-invocable: true\n---"
+
+    def test_chained_calls_both_apply(self):
+        """The exact sequence `post_process_skill_content` runs: a second
+        injected key must still land, not be silently dropped because the
+        first call already destroyed the closing `---` line."""
+        from specify_cli.integrations.claude import ClaudeIntegration
+
+        content = "---\nname: x\n---"
+        result = ClaudeIntegration._inject_frontmatter_flag(
+            content, "user-invocable"
+        )
+        result = ClaudeIntegration._inject_frontmatter_flag(
+            result, "disable-model-invocation", "false"
+        )
+        assert result == (
+            "---\nname: x\nuser-invocable: true\n"
+            "disable-model-invocation: false\n---"
+        )
+
+    def test_preserves_crlf_line_endings(self):
+        """When the closing delimiter *does* end with \\r\\n, the injected
+        line must reuse that EOL rather than switching the file to LF."""
+        from specify_cli.integrations.claude import ClaudeIntegration
+
+        content = "---\r\nname: x\r\n---\r\n"
+        result = ClaudeIntegration._inject_frontmatter_flag(
+            content, "user-invocable"
+        )
+        assert result == "---\r\nname: x\r\nuser-invocable: true\r\n---\r\n"
+
+
 class TestClaudeForkContext:
     """Verify context: fork is injected only for commands listed in FORK_CONTEXT_COMMANDS."""
 

tests/integrations/test_integration_vibe.py

@@ -334,3 +334,53 @@ def test_all_skills_have_disable_model_invocation(self, tmp_path):
             assert parsed.get("disable-model-invocation") is False, (
                 f"{f.parent.name}/SKILL.md is missing disable-model-invocation: false in frontmatter"
             )
+
+
+class TestVibeInjectFrontmatterFlagNoTrailingNewline:
+    """`_inject_frontmatter_flag` must not corrupt content whose closing
+    frontmatter delimiter is the file's last line with no trailing newline.
+
+    `post_process_skill_content` calls this helper on content from
+    "external skill generators (presets, extensions)" (per the base
+    class's docstring) -- not guaranteed to end with a trailing newline.
+    Without a newline after the injected line, the injected text glues
+    onto the closing `---`, destroying the delimiter.
+    """
+
+    def test_single_call_keeps_delimiter_on_its_own_line(self):
+        from specify_cli.integrations.vibe import VibeIntegration
+
+        content = "---\nname: x\n---"
+        result = VibeIntegration._inject_frontmatter_flag(
+            content, "user-invocable"
+        )
+        assert result == "---\nname: x\nuser-invocable: true\n---"
+
+    def test_chained_calls_both_apply(self):
+        """The exact sequence `post_process_skill_content` runs: a second
+        injected key must still land, not be silently dropped because the
+        first call already destroyed the closing `---` line."""
+        from specify_cli.integrations.vibe import VibeIntegration
+
+        content = "---\nname: x\n---"
+        result = VibeIntegration._inject_frontmatter_flag(
+            content, "user-invocable"
+        )
+        result = VibeIntegration._inject_frontmatter_flag(
+            result, "disable-model-invocation", "false"
+        )
+        assert result == (
+            "---\nname: x\nuser-invocable: true\n"
+            "disable-model-invocation: false\n---"
+        )
+
+    def test_preserves_crlf_line_endings(self):
+        """When the closing delimiter *does* end with \\r\\n, the injected
+        line must reuse that EOL rather than switching the file to LF."""
+        from specify_cli.integrations.vibe import VibeIntegration
+
+        content = "---\r\nname: x\r\n---\r\n"
+        result = VibeIntegration._inject_frontmatter_flag(
+            content, "user-invocable"
+        )
+        assert result == "---\r\nname: x\r\nuser-invocable: true\r\n---\r\n"