diff --git a/src/specify_cli/agents.py b/src/specify_cli/agents.py
index b5f018b89a..4a1491c30f 100644
--- a/src/specify_cli/agents.py
+++ b/src/specify_cli/agents.py
@@ -201,33 +201,36 @@ 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/"
+        pattern = re.compile(
+            r"""(^|[\s`"'(\[{<])(\.specify/|(?:\.\./)+|(?:\.?/))?(scripts|memory|templates)/"""
         )
 
+        def _replace(m: re.Match) -> str:
+            prefix = m.group(1)
+            rel = m.group(2)
+            target = m.group(3)
+
+            if rel == ".specify/":
+                # Already normalized to project structure
+                return m.group(0)
+
+            if rel and rel.startswith("../"):
+                # Explicit repo-relative path always maps to root .specify/<target>/
+                return f"{prefix}.specify/{target}/"
+
+            # 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
diff --git a/tests/test_extensions.py b/tests/test_extensions.py
index 800f5ce00e..a790bf0fe7 100644
--- a/tests/test_extensions.py
+++ b/tests/test_extensions.py
@@ -3425,6 +3425,79 @@ 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",
+            ),
+        ]
+
+        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, and parens 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"
+            "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 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_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