fix: ensure idempotent project-relative path rewriting in CommandRegistrar (#4553)

* fix: ensure idempotent project-relative path rewriting in CommandRegistrar

Replace the fragile pattern of three sequential string replacements followed by three re.sub calls and trailing `.replace(".specify/.specify/", ".specify/")` / `.replace(".specify.specify/", ".specify/")` patches in CommandRegistrar.rewrite_project_relative_paths.

Consolidate the transformation into a unified regex match callback that:
- Inspects matched path prefixes (`.specify/`, `../`, `./`, `/`, or bare)
- Naturally guards already-normalized `.specify/` paths from double-prefixing
- Directs parent relative references (`../`) to root `.specify/<target>/`
- Preserves extension-local script scoping when extension_id is provided
- Expands boundary delimiters to include Markdown brackets, parentheses, braces, angle brackets, and backticks

Add unit tests in tests/test_extensions.py covering repeated passes for idempotency, markdown enclosure delimiters, and edge-case inputs.

Assisted-by: Antigravity (supervised)

* fix: preserve parent-relative paths following = in rewrite_project_relative_paths

Extend the delimiter boundary character class in CommandRegistrar.rewrite_project_relative_paths
to include '=', ensuring option flags (e.g., '--template=../../templates/spec.md') and
environment variable assignments (e.g., 'SCRIPT=../../scripts/bash/run.sh') continue to
be rewritten properly.

Add regression test coverage in tests/test_extensions.py covering '=' assignments and
verifying repeated passes for idempotency.

Assisted-by: Google Antigravity (model: Gemini 3.8 Flash, supervised)

* fix: rewrite parent-relative paths after punctuation separators

The delimiter allowlist skipped inputs such as run;../../scripts. Match
../ independently of that list, keep the boundary guard for bare paths,
and add punctuation/shell-operator regression cases.

Assisted-by: Google Antigravity (model: Gemini 3.8 Flash, supervised)

* fix: require two parent segments before repo-root rewrites

A single ../ is one directory up, not the repository root. Match
(?:\.\./){2,} so ../scripts/ stays unchanged even with extension_id,
while ../../ and deeper still map to .specify/<target>/.

Assisted-by: Grok 4.7 (model: grok-4.7, autonomous)

Author: darion-yaphet

src/specify_cli/agents.py

@@ -201,33 +201,47 @@ def rewrite_project_relative_paths(
         if not isinstance(text, str) or not text:
             return text
 
-        for old, new in (
-            ("../../memory/", ".specify/memory/"),
-            ("../../scripts/", ".specify/scripts/"),
-            ("../../templates/", ".specify/templates/"),
-        ):
-            text = text.replace(old, new)
-
-        # Only rewrite top-level style references so existing generated paths
-        # like ".specify/extensions/<ext>/scripts/..." remain intact. When
-        # rendering extension commands, top-level "scripts/" is extension-local.
         scripts_replacement = (
             f".specify/extensions/{extension_id}/scripts/"
             if extension_id
             else ".specify/scripts/"
         )
-        text = re.sub(r'(^|[\s`"\'(])(?:\.?/)?memory/', r"\1.specify/memory/", text)
-        text = re.sub(
-            r'(^|[\s`"\'(])(?:\.?/)?scripts/', rf"\1{scripts_replacement}", text
-        )
-        text = re.sub(
-            r'(^|[\s`"\'(])(?:\.?/)?templates/', r"\1.specify/templates/", text
-        )
 
-        return text.replace(".specify/.specify/", ".specify/").replace(
-            ".specify.specify/", ".specify/"
+        # Two or more ``../`` segments are the repo-root signal used by
+        # command templates (``../../scripts/...``) and are matched without
+        # the delimiter allowlist. A single ``../`` stays untouched: from a
+        # nested command file it means one directory up, which is not the
+        # repository root and must not be routed to ``.specify/scripts/``.
+        # A lookbehind only rejects identifier/dot glue (``not../scripts/``,
+        # ``..../scripts/``). Bare ``scripts/`` / ``memory/`` / ``templates/``
+        # still require a recognized boundary so tokens such as
+        # ``myscripts/`` are not rewritten.
+        pattern = re.compile(
+            r"""(?:(?<![.\w])(?P<parent>(?:\.\./){2,})|(?P<boundary>^|[\s`"'(\[{<=])(?P<rel>\.specify/|(?:\.?/))?)(?P<target>scripts|memory|templates)/"""
         )
 
+        def _replace(m: re.Match) -> str:
+            target = m.group("target")
+
+            if m.group("parent"):
+                # Two or more ../ segments always map to root .specify/<target>/,
+                # including when extension_id would otherwise make scripts/ local.
+                return f".specify/{target}/"
+
+            prefix = m.group("boundary")
+            rel = m.group("rel")
+
+            if rel == ".specify/":
+                # Already normalized to project structure
+                return m.group(0)
+
+            # Top-level or ./ path
+            if target == "scripts":
+                return f"{prefix}{scripts_replacement}"
+            return f"{prefix}.specify/{target}/"
+
+        return pattern.sub(_replace, text)
+
     @staticmethod
     def rewrite_extension_paths(
         text: str, extension_id: str, extension_dir: Path

tests/test_extensions.py

@@ -3512,6 +3512,159 @@ def test_rewrite_project_relative_paths_uses_extension_context_for_scripts(self)
         assert ".specify/scripts/bash/setup-plan.sh" in rewritten
         assert ".specify/templates/checklist.md" in rewritten
 
+    def test_rewrite_project_relative_paths_idempotency(self):
+        """Repeated applications must produce identical results with no double prefixing."""
+        from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar
+
+        samples = [
+            ("Run scripts/bash/setup-plan.sh --json", None, "Run .specify/scripts/bash/setup-plan.sh --json"),
+            ("Run ./scripts/bash/setup-plan.sh --json", None, "Run .specify/scripts/bash/setup-plan.sh --json"),
+            ("Run ../../scripts/bash/setup-plan.sh", None, "Run .specify/scripts/bash/setup-plan.sh"),
+            ("Run ../../../scripts/bash/setup-plan.sh", None, "Run .specify/scripts/bash/setup-plan.sh"),
+            ("Read memory/constitution.md", None, "Read .specify/memory/constitution.md"),
+            ("Read /memory/constitution.md", None, "Read .specify/memory/constitution.md"),
+            ("Read ./memory/constitution.md", None, "Read .specify/memory/constitution.md"),
+            ("Read ../../memory/constitution.md", None, "Read .specify/memory/constitution.md"),
+            ("Read templates/spec.md", None, "Read .specify/templates/spec.md"),
+            ("Read ./templates/spec.md", None, "Read .specify/templates/spec.md"),
+            ("Read ../../templates/spec.md", None, "Read .specify/templates/spec.md"),
+            ("Run .specify/scripts/bash/setup-plan.sh", None, "Run .specify/scripts/bash/setup-plan.sh"),
+            ("Read .specify/memory/constitution.md", None, "Read .specify/memory/constitution.md"),
+            ("Read .specify/templates/spec.md", None, "Read .specify/templates/spec.md"),
+            ("Run scripts/tool.sh", "my-ext", "Run .specify/extensions/my-ext/scripts/tool.sh"),
+            ("Run ./scripts/tool.sh", "my-ext", "Run .specify/extensions/my-ext/scripts/tool.sh"),
+            ("Run ../../scripts/tool.sh", "my-ext", "Run .specify/scripts/tool.sh"),
+            (
+                "Run .specify/extensions/my-ext/scripts/tool.sh",
+                "my-ext",
+                "Run .specify/extensions/my-ext/scripts/tool.sh",
+            ),
+            (
+                "--template=../../templates/spec.md",
+                None,
+                "--template=.specify/templates/spec.md",
+            ),
+            (
+                "SCRIPT=../../scripts/bash/run.sh",
+                None,
+                "SCRIPT=.specify/scripts/bash/run.sh",
+            ),
+            (
+                "--template=templates/spec.md",
+                None,
+                "--template=.specify/templates/spec.md",
+            ),
+            (
+                "SCRIPT=scripts/bash/run.sh",
+                "my-ext",
+                "SCRIPT=.specify/extensions/my-ext/scripts/bash/run.sh",
+            ),
+        ]
+
+        for text, ext_id, expected in samples:
+            once = AgentCommandRegistrar.rewrite_project_relative_paths(text, extension_id=ext_id)
+            assert once == expected
+            twice = AgentCommandRegistrar.rewrite_project_relative_paths(once, extension_id=ext_id)
+            assert twice == expected
+            thrice = AgentCommandRegistrar.rewrite_project_relative_paths(twice, extension_id=ext_id)
+            assert thrice == expected
+            assert ".specify/.specify/" not in thrice
+            assert ".specify.specify/" not in thrice
+
+    def test_rewrite_project_relative_paths_various_delimiters(self):
+        """Paths enclosed by backticks, quotes, brackets, parens, and = should be rewritten."""
+        from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar
+
+        body = (
+            "Inline `scripts/bash/run.sh` and \"scripts/bash/run.sh\" and 'scripts/bash/run.sh'\n"
+            "Parens (scripts/bash/run.sh) and brackets [scripts/bash/run.sh]\n"
+            "Braces {scripts/bash/run.sh} and angles <scripts/bash/run.sh>\n"
+            "Flag --template=../../templates/spec.md and assign SCRIPT=../../scripts/bash/run.sh\n"
+            "Start of text: scripts/bash/run.sh\n"
+        )
+        rewritten = AgentCommandRegistrar.rewrite_project_relative_paths(body)
+
+        assert "`.specify/scripts/bash/run.sh`" in rewritten
+        assert "\".specify/scripts/bash/run.sh\"" in rewritten
+        assert "'.specify/scripts/bash/run.sh'" in rewritten
+        assert "(.specify/scripts/bash/run.sh)" in rewritten
+        assert "[.specify/scripts/bash/run.sh]" in rewritten
+        assert "{.specify/scripts/bash/run.sh}" in rewritten
+        assert "<.specify/scripts/bash/run.sh>" in rewritten
+        assert "--template=.specify/templates/spec.md" in rewritten
+        assert "SCRIPT=.specify/scripts/bash/run.sh" in rewritten
+        assert rewritten.splitlines()[-1] == "Start of text: .specify/scripts/bash/run.sh"
+
+        # Verify idempotency on multiline text with diverse delimiters
+        again = AgentCommandRegistrar.rewrite_project_relative_paths(rewritten)
+        assert again == rewritten
+        assert ".specify/.specify/" not in again
+
+    def test_rewrite_project_relative_paths_punctuation_and_shell_operator_boundaries(self):
+        """Parent-relative paths rewrite after punctuation/shell operators.
+
+        Two or more ``../`` segments are a repo-root signal and must not
+        depend on the delimiter allowlist. A single ``../`` stays untouched,
+        including when ``extension_id`` is set, so it is not routed to root
+        ``.specify/scripts/`` or to extension-local scripts. Bare
+        ``scripts/`` / ``templates/`` / ``memory/`` paths still require a
+        recognized boundary so ``myscripts/`` and ``run;scripts/`` stay
+        untouched.
+        """
+        from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar
+
+        samples = [
+            ("run;../../scripts/a.sh", None, "run;.specify/scripts/a.sh"),
+            ("path:../../templates/a.md", None, "path:.specify/templates/a.md"),
+            ("run&&../../scripts/a.sh", None, "run&&.specify/scripts/a.sh"),
+            ("run||../../scripts/a.sh", None, "run||.specify/scripts/a.sh"),
+            ("cmd|../../scripts/a.sh", None, "cmd|.specify/scripts/a.sh"),
+            ("x,../../memory/constitution.md", None, "x,.specify/memory/constitution.md"),
+            ("run;../../../scripts/a.sh", None, "run;.specify/scripts/a.sh"),
+            (
+                "run;../../scripts/a.sh",
+                "my-ext",
+                "run;.specify/scripts/a.sh",
+            ),
+            (
+                "foo/../../scripts/a.sh",
+                None,
+                "foo/.specify/scripts/a.sh",
+            ),
+            # Bare paths still need a recognized boundary.
+            ("run;scripts/a.sh", None, "run;scripts/a.sh"),
+            ("path:templates/a.md", None, "path:templates/a.md"),
+            ("run&&scripts/a.sh", None, "run&&scripts/a.sh"),
+            ("myscripts/a.sh", None, "myscripts/a.sh"),
+            # ``../`` must not match inside an identifier or extra dots.
+            ("not../scripts/a.sh", None, "not../scripts/a.sh"),
+            ("..../scripts/a.sh", None, "..../scripts/a.sh"),
+            # One ``../`` is one directory up, not the repository root.
+            ("Run ../scripts/a.sh", None, "Run ../scripts/a.sh"),
+            ("Run ../scripts/a.sh", "my-ext", "Run ../scripts/a.sh"),
+            ("run;../scripts/a.sh", "my-ext", "run;../scripts/a.sh"),
+            ("Read ../memory/constitution.md", "my-ext", "Read ../memory/constitution.md"),
+            ("Read ../templates/spec.md", "my-ext", "Read ../templates/spec.md"),
+        ]
+
+        for text, ext_id, expected in samples:
+            once = AgentCommandRegistrar.rewrite_project_relative_paths(
+                text, extension_id=ext_id
+            )
+            assert once == expected, text
+            twice = AgentCommandRegistrar.rewrite_project_relative_paths(
+                once, extension_id=ext_id
+            )
+            assert twice == expected, text
+
+    def test_rewrite_project_relative_paths_non_string_or_empty(self):
+        """Non-string and falsy inputs should be returned as-is."""
+        from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar
+
+        assert AgentCommandRegistrar.rewrite_project_relative_paths("") == ""
+        assert AgentCommandRegistrar.rewrite_project_relative_paths(None) is None
+        assert AgentCommandRegistrar.rewrite_project_relative_paths(123) == 123
+
     def test_render_toml_command_handles_embedded_triple_double_quotes(self):
         """TOML renderer should stay valid when body includes triple double-quotes."""
         from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar