diff --git a/src/fastcontext/agent/agent.py b/src/fastcontext/agent/agent.py
index 478e93f..922bbcd 100644
--- a/src/fastcontext/agent/agent.py
+++ b/src/fastcontext/agent/agent.py
@@ -72,7 +72,7 @@ async def _agent_loop(self, prompt: str, max_turns: int, verbose: bool, citation
                 await self.context.add(tools_result_msg)
             else:
                 if citation:
-                    return get_final_answer(step_msg.content)
+                    return get_final_answer(step_msg.content, work_dir=self.work_dir)
                 return step_msg.content
 
     async def run(self, prompt: str, max_turns: int = 4, verbose: bool = False, citation: bool = False) -> str:
diff --git a/src/fastcontext/agent/tool/glob.py b/src/fastcontext/agent/tool/glob.py
index 4506346..749ca05 100644
--- a/src/fastcontext/agent/tool/glob.py
+++ b/src/fastcontext/agent/tool/glob.py
@@ -3,7 +3,7 @@
 from pathlib import Path
 
 from .tool import Tool
-from .utils import RG_PATH
+from .utils import RG_PATH, resolve_path
 
 
 def run(directory: str, pattern: str, cwd: str) -> str:
@@ -46,6 +46,23 @@ async def call(self, parameters: str, **kwargs) -> str:
         directory = params.get("directory", cwd)
         pattern = params.get("pattern")
 
+        directory = resolve_path(directory, cwd)
+
+        # The model sometimes puts a full path in the pattern parameter
+        # (e.g. /myrepo/backend/**/*.py instead of just **/*.py)
+        if pattern and pattern.startswith("/"):
+            cwd_name = Path(cwd).name
+            prefix = f"/{cwd_name}/"
+            if pattern.startswith(prefix):
+                pattern = pattern[len(prefix):]
+            else:
+                parts = pattern.split("/")
+                glob_chars = {"*", "?", "[", "{"}
+                for i, part in enumerate(parts):
+                    if any(c in part for c in glob_chars):
+                        pattern = "/".join(parts[i:])
+                        break
+
         p = Path(directory)
         if not p.is_dir():
             return f"<system-reminder>Error: directory `{directory}` does not exist or is not a directory.</system-reminder>"
diff --git a/src/fastcontext/agent/tool/grep.py b/src/fastcontext/agent/tool/grep.py
index 4ee161f..47a69bf 100644
--- a/src/fastcontext/agent/tool/grep.py
+++ b/src/fastcontext/agent/tool/grep.py
@@ -2,7 +2,7 @@
 from pathlib import Path
 
 from .tool import Tool
-from .utils import RG_PATH
+from .utils import RG_PATH, resolve_path
 
 
 class GrepTool(Tool):
@@ -82,6 +82,8 @@ async def call(self, parameters: str, **kwargs) -> str:
         head_limit = params.get("head_limit")
         multiline = params.get("multiline")
 
+        path = resolve_path(path, cwd)
+
         if not Path(path).resolve().is_relative_to(Path(cwd).resolve()):
             return f"<system-reminder>Permission error: `{path}` is not within the working directory `{cwd}`</system-reminder>"
 
diff --git a/src/fastcontext/agent/tool/read.py b/src/fastcontext/agent/tool/read.py
index a0caa76..34c7a62 100644
--- a/src/fastcontext/agent/tool/read.py
+++ b/src/fastcontext/agent/tool/read.py
@@ -4,6 +4,7 @@
 import aiofiles
 
 from .tool import Tool
+from .utils import resolve_path
 
 MAX_LINE = 2000
 MAX_LINE_LENGTH = 2000
@@ -41,12 +42,18 @@ async def call(self, parameters: str, **kwargs) -> str:
             return "<system-reminder>Error: file path is required</system-reminder>"
 
         cwd = kwargs.get("cwd", Path.cwd().as_posix())
+
+        file_path = resolve_path(file_path, cwd)
+
         if not Path(file_path).resolve().is_relative_to(Path(cwd).resolve()):
             return f"<system-reminder>Permission error: `{file_path}` is not within the working directory `{cwd}`</system-reminder>"
 
         if not Path(file_path).exists():
             return f"<system-reminder>Error: {file_path} does not exist</system-reminder>"
 
+        if Path(file_path).is_dir():
+            return f"<system-reminder>Error: {file_path} is a directory, not a file. Use Glob to find files in this directory.</system-reminder>"
+
         if not isinstance(offset, int) or offset <= 0:
             return "<system-reminder>Error: offset must be a positive integer</system-reminder>"
 
diff --git a/src/fastcontext/agent/tool/utils.py b/src/fastcontext/agent/tool/utils.py
index 8deaddb..8e44966 100644
--- a/src/fastcontext/agent/tool/utils.py
+++ b/src/fastcontext/agent/tool/utils.py
@@ -1,6 +1,7 @@
 import os
 import platform
 import shutil
+from pathlib import Path
 
 
 def _find_existing_rg() -> str | None:
@@ -12,3 +13,46 @@ def _find_existing_rg() -> str | None:
 
 
 RG_PATH = _find_existing_rg()
+
+
+def resolve_path(file_path: str, cwd: str) -> str:
+    """Resolve short-prefixed model path to full absolute path.
+
+    Model prefix path with last cwd component: emit ``/myrepo/src`` not
+    ``/home/user/projects/myrepo/src``. Rewrite to full form so tool
+    permission check (``is_relative_to(cwd)``) pass. Already within cwd:
+    return unchanged.
+    """
+    cwd_path = Path(cwd).resolve()
+
+    try:
+        if Path(file_path).resolve().is_relative_to(cwd_path) and Path(file_path).exists():
+            return file_path
+    except (OSError, ValueError):
+        pass
+
+    # Model used last cwd component as prefix:
+    # cwd=/home/user/projects/myrepo, model says /myrepo/src/...
+    cwd_name = cwd_path.name
+    prefix = f"/{cwd_name}/"
+    if file_path.startswith(prefix):
+        candidate = cwd_path / file_path[len(prefix):]
+        return str(candidate.resolve())
+
+    if file_path == f"/{cwd_name}":
+        return str(cwd_path)
+
+    if file_path.startswith("/"):
+        relative = file_path.lstrip("/")
+        candidate = cwd_path / relative
+        if candidate.exists():
+            return str(candidate.resolve())
+
+    parts = Path(file_path).parts
+    for i in range(1, len(parts)):
+        suffix = Path(*parts[i:])
+        candidate = cwd_path / suffix
+        if candidate.exists():
+            return str(candidate.resolve())
+
+    return file_path
diff --git a/src/fastcontext/agent/utils.py b/src/fastcontext/agent/utils.py
index b43f921..e86109f 100644
--- a/src/fastcontext/agent/utils.py
+++ b/src/fastcontext/agent/utils.py
@@ -56,7 +56,7 @@ def load_system_prompt(work_dir: str) -> str:
 def parse_citations(text: str) -> list:
     final_answer = re.search(r"<final_answer>(.*?)</final_answer>", text, re.DOTALL)
     if final_answer is None:
-        return {"final_answer": text.strip(), "citations": []}
+        return []
 
     entries = final_answer.group(1).strip().splitlines()
 
@@ -87,14 +87,20 @@ def parse_citations(text: str) -> list:
     return citations
 
 
-def format_citations(citations: list, validate: bool = True) -> str:
+def format_citations(citations: list, validate: bool = True, work_dir: str = None) -> str:
 
     if validate:
+        from fastcontext.agent.tool.utils import resolve_path
+
         validated_citations = []
         for c in citations:
-            # if not file or not existing, skip this citation
-            if not os.path.isfile(c["path"]):
+            path = c["path"]
+            if work_dir:
+                path = resolve_path(path, work_dir)
+            if not os.path.isfile(path):
                 continue
+            c = dict(c)
+            c["path"] = path
             validated_citations.append(c)
 
         citations = validated_citations
@@ -108,9 +114,9 @@ def format_citations(citations: list, validate: bool = True) -> str:
     return "<final_answer>\n" + "\n".join(formatted) + "\n</final_answer>"
 
 
-def get_final_answer(text: str) -> str:
+def get_final_answer(text: str, work_dir: str = None) -> str:
     citations = parse_citations(text)
-    final_answer = format_citations(citations)
+    final_answer = format_citations(citations, work_dir=work_dir)
     return final_answer
 
 
diff --git a/tests/test_path_resolution.py b/tests/test_path_resolution.py
new file mode 100644
index 0000000..00c42e4
--- /dev/null
+++ b/tests/test_path_resolution.py
@@ -0,0 +1,32 @@
+"""Tests for the resolve_path helper."""
+
+from pathlib import Path
+
+import pytest
+
+from fastcontext.agent.tool.utils import resolve_path
+
+
+@pytest.fixture
+def cwd(tmp_path):
+    repo = tmp_path / "projects" / "myrepo"
+    (repo / "backend").mkdir(parents=True)
+    (repo / "backend" / "main.py").write_text("print('hello')\n")
+    return str(repo)
+
+
+class TestResolvePath:
+    def test_already_absolute_within_cwd(self, cwd):
+        full_path = str(Path(cwd) / "backend" / "main.py")
+        assert resolve_path(full_path, cwd) == full_path
+
+    def test_short_prefix_resolution(self, cwd):
+        result = resolve_path("/myrepo/backend/main.py", cwd)
+        assert result == str(Path(cwd) / "backend" / "main.py")
+
+    def test_unresolvable_path_returns_original(self, cwd):
+        assert resolve_path("/nope/file.py", cwd) == "/nope/file.py"
+
+    def test_suffix_matching(self, cwd):
+        result = resolve_path("/some/random/prefix/backend/main.py", cwd)
+        assert result == str(Path(cwd) / "backend" / "main.py")