diff --git a/codeflash/cli_cmds/init_javascript.py b/codeflash/cli_cmds/init_javascript.py
index d88c69904..e43bdc167 100644
--- a/codeflash/cli_cmds/init_javascript.py
+++ b/codeflash/cli_cmds/init_javascript.py
@@ -128,7 +128,7 @@ def determine_js_package_manager(project_root: Path) -> JsPackageManager:
     """
     # Search from project_root up to filesystem root for lock files
     # This supports monorepo setups where lock file is at workspace root
-    current_dir = project_root.resolve()
+    current_dir = project_root
     while current_dir != current_dir.parent:
         if (current_dir / "bun.lockb").exists() or (current_dir / "bun.lock").exists():
             return JsPackageManager.BUN
@@ -161,7 +161,7 @@ def find_node_modules_with_package(project_root: Path, package_name: str) -> Pat
         Path to the node_modules directory containing the package, or None if not found.
 
     """
-    current_dir = project_root.resolve()
+    current_dir = project_root
     while current_dir != current_dir.parent:
         node_modules = current_dir / "node_modules"
         if node_modules.exists():
diff --git a/codeflash/code_utils/instrument_existing_tests.py b/codeflash/code_utils/instrument_existing_tests.py
index 9486fc677..f15b2d56a 100644
--- a/codeflash/code_utils/instrument_existing_tests.py
+++ b/codeflash/code_utils/instrument_existing_tests.py
@@ -709,6 +709,7 @@ def inject_profiling_into_existing_test(
     tests_project_root: Path,
     mode: TestingMode = TestingMode.BEHAVIOR,
 ) -> tuple[bool, str | None]:
+    tests_project_root = tests_project_root.resolve()
     if function_to_optimize.is_async:
         return inject_async_profiling_into_existing_test(
             test_path, call_positions, function_to_optimize, tests_project_root, mode
diff --git a/codeflash/discovery/discover_unit_tests.py b/codeflash/discovery/discover_unit_tests.py
index d1ef28a8d..1a032ec36 100644
--- a/codeflash/discovery/discover_unit_tests.py
+++ b/codeflash/discovery/discover_unit_tests.py
@@ -69,8 +69,8 @@ class TestFunction:
 class TestsCache:
     SCHEMA_VERSION = 1  # Increment this when schema changes
 
-    def __init__(self, project_root_path: str | Path) -> None:
-        self.project_root_path = Path(project_root_path).resolve().as_posix()
+    def __init__(self, project_root_path: Path) -> None:
+        self.project_root_path = project_root_path.resolve().as_posix()
         self.connection = sqlite3.connect(codeflash_cache_db)
         self.cur = self.connection.cursor()
 
diff --git a/codeflash/discovery/functions_to_optimize.py b/codeflash/discovery/functions_to_optimize.py
index ed18ed53b..14455b890 100644
--- a/codeflash/discovery/functions_to_optimize.py
+++ b/codeflash/discovery/functions_to_optimize.py
@@ -836,6 +836,7 @@ def filter_functions(
     *,
     disable_logs: bool = False,
 ) -> tuple[dict[Path, list[FunctionToOptimize]], int]:
+    resolved_project_root = project_root.resolve()
     filtered_modified_functions: dict[str, list[FunctionToOptimize]] = {}
     blocklist_funcs = get_blocklisted_functions()
     logger.debug(f"Blocklisted functions: {blocklist_funcs}")
@@ -912,7 +913,7 @@ def is_test_file(file_path_normalized: str) -> bool:
         lang_support = get_language_support(Path(file_path))
         if lang_support.language == Language.PYTHON:
             try:
-                ast.parse(f"import {module_name_from_file_path(Path(file_path), project_root)}")
+                ast.parse(f"import {module_name_from_file_path(Path(file_path), resolved_project_root)}")
             except SyntaxError:
                 malformed_paths_count += 1
                 continue
@@ -934,7 +935,10 @@ def is_test_file(file_path_normalized: str) -> bool:
         if previous_checkpoint_functions:
             functions_tmp = []
             for function in _functions:
-                if function.qualified_name_with_modules_from_root(project_root) in previous_checkpoint_functions:
+                if (
+                    function.qualified_name_with_modules_from_root(resolved_project_root)
+                    in previous_checkpoint_functions
+                ):
                     previous_checkpoint_functions_removed_count += 1
                     continue
                 functions_tmp.append(function)
diff --git a/codeflash/languages/javascript/import_resolver.py b/codeflash/languages/javascript/import_resolver.py
index 8f5dbe8ca..b5ec67115 100644
--- a/codeflash/languages/javascript/import_resolver.py
+++ b/codeflash/languages/javascript/import_resolver.py
@@ -44,8 +44,7 @@ def __init__(self, project_root: Path) -> None:
             project_root: Root directory of the project.
 
         """
-        # Resolve to real path to handle macOS symlinks like /var -> /private/var
-        self.project_root = project_root.resolve()
+        self.project_root = project_root
         self._resolution_cache: dict[tuple[Path, str], Path | None] = {}
 
     def resolve_import(self, import_info: ImportInfo, source_file: Path) -> ResolvedImport | None:
diff --git a/codeflash/languages/python/context/code_context_extractor.py b/codeflash/languages/python/context/code_context_extractor.py
index 09b045dcc..9a4daf726 100644
--- a/codeflash/languages/python/context/code_context_extractor.py
+++ b/codeflash/languages/python/context/code_context_extractor.py
@@ -2,7 +2,6 @@
 
 import ast
 import hashlib
-import os
 from collections import defaultdict
 from itertools import chain
 from pathlib import Path
@@ -512,6 +511,10 @@ def get_function_sources_from_jedi(
                     # TODO: there can be multiple definitions, see how to handle such cases
                     definition = definitions[0]
                     definition_path = definition.module_path
+                    if definition_path is not None:
+                        rel = safe_relative_to(definition_path, project_root_path)
+                        if not rel.is_absolute():
+                            definition_path = project_root_path / rel
 
                     # The definition is part of this project and not defined within the original function
                     is_valid_definition = (
@@ -936,7 +939,11 @@ def is_project_path(module_path: Path | None, project_root_path: Path) -> bool:
     # site-packages must be checked first because .venv/site-packages is under project root
     if path_belongs_to_site_packages(module_path):
         return False
-    return str(module_path).startswith(str(project_root_path) + os.sep)
+    try:
+        module_path.resolve().relative_to(project_root_path.resolve())
+        return True
+    except ValueError:
+        return False
 
 
 def _is_project_module(module_name: str, project_root_path: Path) -> bool:
diff --git a/codeflash/languages/python/context/unused_definition_remover.py b/codeflash/languages/python/context/unused_definition_remover.py
index 38b58f63e..ba6e4d549 100644
--- a/codeflash/languages/python/context/unused_definition_remover.py
+++ b/codeflash/languages/python/context/unused_definition_remover.py
@@ -587,17 +587,20 @@ def revert_unused_helper_functions(
 
     logger.debug(f"Reverting {len(unused_helpers)} unused helper function(s) to original definitions")
 
+    # Resolve all path keys for consistent comparison (Windows 8.3 short names may differ from Jedi-resolved paths)
+    resolved_original_helper_code = {p.resolve(): code for p, code in original_helper_code.items()}
+
     # Group unused helpers by file path
     unused_helpers_by_file = defaultdict(list)
     for helper in unused_helpers:
-        unused_helpers_by_file[helper.file_path].append(helper)
+        unused_helpers_by_file[helper.file_path.resolve()].append(helper)
 
     # For each file, revert the unused helper functions to their original definitions
     for file_path, helpers_in_file in unused_helpers_by_file.items():
-        if file_path in original_helper_code:
+        if file_path in resolved_original_helper_code:
             try:
                 # Get original code for this file
-                original_code = original_helper_code[file_path]
+                original_code = resolved_original_helper_code[file_path]
 
                 # Use the code replacer to selectively revert only the unused helper functions
                 helper_names = [helper.qualified_name for helper in helpers_in_file]
diff --git a/codeflash/optimization/function_optimizer.py b/codeflash/optimization/function_optimizer.py
index 7cbcda976..c24d84ae5 100644
--- a/codeflash/optimization/function_optimizer.py
+++ b/codeflash/optimization/function_optimizer.py
@@ -2,6 +2,7 @@
 
 import ast
 import concurrent.futures
+import dataclasses
 import logging
 import os
 import queue
@@ -443,9 +444,12 @@ def __init__(
         args: Namespace | None = None,
         replay_tests_dir: Path | None = None,
     ) -> None:
-        self.project_root = test_cfg.project_root_path
+        self.project_root = test_cfg.project_root_path.resolve()
         self.test_cfg = test_cfg
         self.aiservice_client = aiservice_client if aiservice_client else AiServiceClient()
+        resolved_file_path = function_to_optimize.file_path.resolve()
+        if resolved_file_path != function_to_optimize.file_path:
+            function_to_optimize = dataclasses.replace(function_to_optimize, file_path=resolved_file_path)
         self.function_to_optimize = function_to_optimize
         self.function_to_optimize_source_code = (
             function_to_optimize_source_code
@@ -1451,7 +1455,7 @@ def reformat_code_and_helpers(
         optimized_code = ""
         if optimized_context is not None:
             file_to_code_context = optimized_context.file_to_path()
-            optimized_code = file_to_code_context.get(str(path.relative_to(self.project_root)), "")
+            optimized_code = file_to_code_context.get(str(path.resolve().relative_to(self.project_root)), "")
 
         new_code = format_code(
             self.args.formatter_cmds, path, optimized_code=optimized_code, check_diff=True, exit_on_failure=False
diff --git a/codeflash/result/create_pr.py b/codeflash/result/create_pr.py
index 0be4e1cf8..b276725f2 100644
--- a/codeflash/result/create_pr.py
+++ b/codeflash/result/create_pr.py
@@ -126,10 +126,10 @@ def existing_tests_source_for(
             tests_dir_name = test_cfg.tests_project_rootdir.name
             if file_path.startswith((tests_dir_name + os.sep, tests_dir_name + "/")):
                 # Module path includes "tests." - use project root parent
-                instrumented_abs_path = (test_cfg.tests_project_rootdir.parent / file_path).resolve()
+                instrumented_abs_path = test_cfg.tests_project_rootdir.parent / file_path
             else:
                 # Module path doesn't include tests dir - use tests root directly
-                instrumented_abs_path = (test_cfg.tests_project_rootdir / file_path).resolve()
+                instrumented_abs_path = test_cfg.tests_project_rootdir / file_path
             logger.debug(f"[PR-DEBUG] Looking up: {instrumented_abs_path}")
             logger.debug(f"[PR-DEBUG]   Available keys: {list(instrumented_to_original.keys())[:3]}")
             # Try to map instrumented path to original path
diff --git a/codeflash/telemetry/sentry.py b/codeflash/telemetry/sentry.py
index 2357439dc..3ee266326 100644
--- a/codeflash/telemetry/sentry.py
+++ b/codeflash/telemetry/sentry.py
@@ -2,6 +2,7 @@
 
 import sentry_sdk
 from sentry_sdk.integrations.logging import LoggingIntegration
+from sentry_sdk.integrations.stdlib import StdlibIntegration
 
 
 def init_sentry(*, enabled: bool = False, exclude_errors: bool = False) -> None:
@@ -16,12 +17,8 @@ def init_sentry(*, enabled: bool = False, exclude_errors: bool = False) -> None:
         sentry_sdk.init(
             dsn="https://4b9a1902f9361b48c04376df6483bc96@o4506833230561280.ingest.sentry.io/4506833262477312",
             integrations=[sentry_logging],
-            # Set traces_sample_rate to 1.0 to capture 100%
-            # of transactions for performance monitoring.
-            traces_sample_rate=1.0,
-            # Set profiles_sample_rate to 1.0 to profile 100%
-            # of sampled transactions.
-            # We recommend adjusting this value in production.
-            profiles_sample_rate=1.0,
+            disabled_integrations=[StdlibIntegration],
+            traces_sample_rate=0,
+            profiles_sample_rate=0,
             ignore_errors=[KeyboardInterrupt],
         )
diff --git a/codeflash/verification/parse_test_output.py b/codeflash/verification/parse_test_output.py
index 4c2c809eb..53012feb1 100644
--- a/codeflash/verification/parse_test_output.py
+++ b/codeflash/verification/parse_test_output.py
@@ -47,8 +47,24 @@ def parse_func(file_path: Path) -> XMLParser:
     return parse(file_path, xml_parser)
 
 
-matches_re_start = re.compile(r"!\$######(.*?):(.*?)([^\.:]*?):(.*?):(.*?):(.*?)######\$!\n")
-matches_re_end = re.compile(r"!######(.*?):(.*?)([^\.:]*?):(.*?):(.*?):(.*?)######!")
+matches_re_start = re.compile(
+    r"!\$######([^:]*)"  # group 1: module path
+    r":((?:[^:.]*\.)*)"  # group 2: class prefix with trailing dot, or empty
+    r"([^.:]*)"  # group 3: test function name
+    r":([^:]*)"  # group 4: function being tested
+    r":([^:]*)"  # group 5: loop index
+    r":([^#]*)"  # group 6: iteration id
+    r"######\$!\n"
+)
+matches_re_end = re.compile(
+    r"!######([^:]*)"  # group 1: module path
+    r":((?:[^:.]*\.)*)"  # group 2: class prefix with trailing dot, or empty
+    r"([^.:]*)"  # group 3: test function name
+    r":([^:]*)"  # group 4: function being tested
+    r":([^:]*)"  # group 5: loop index
+    r":([^#]*)"  # group 6: iteration_id or iteration_id:runtime
+    r"######!"
+)
 
 
 start_pattern = re.compile(r"!\$######([^:]*):([^:]*):([^:]*):([^:]*):([^:]+)######\$!")
@@ -893,7 +909,6 @@ def merge_test_results(
     return merged_test_results
 
 
-FAILURES_HEADER_RE = re.compile(r"=+ FAILURES =+")
 TEST_HEADER_RE = re.compile(r"_{3,}\s*(.*?)\s*_{3,}$")
 
 
@@ -903,7 +918,7 @@ def parse_test_failures_from_stdout(stdout: str) -> dict[str, str]:
     start = end = None
 
     for i, line in enumerate(lines):
-        if FAILURES_HEADER_RE.search(line.strip()):
+        if "= FAILURES =" in line:
             start = i
             break
 
diff --git a/codeflash/verification/verification_utils.py b/codeflash/verification/verification_utils.py
index c567e6a9a..d586d9962 100644
--- a/codeflash/verification/verification_utils.py
+++ b/codeflash/verification/verification_utils.py
@@ -158,6 +158,10 @@ class TestConfig:
     _language: Optional[str] = None  # Language identifier for multi-language support
     js_project_root: Optional[Path] = None  # JavaScript project root (directory containing package.json)
 
+    def __post_init__(self) -> None:
+        self.project_root_path = self.project_root_path.resolve()
+        self.tests_project_rootdir = self.tests_project_rootdir.resolve()
+
     @property
     def test_framework(self) -> str:
         """Returns the appropriate test framework based on language.
diff --git a/pyproject.toml b/pyproject.toml
index fe96c54cb..56736fc6c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -207,6 +207,8 @@ warn_unreachable = true
 install_types = true
 plugins = ["pydantic.mypy"]
 
+exclude = ["tests/", "code_to_optimize/", "pie_test_set/", "experiments/"]
+
 [[tool.mypy.overrides]]
 module = ["jedi", "jedi.api.classes", "inquirer", "inquirer.themes", "numba"]
 ignore_missing_imports = true
diff --git a/tests/test_parse_test_output_regex.py b/tests/test_parse_test_output_regex.py
new file mode 100644
index 000000000..e313885ab
--- /dev/null
+++ b/tests/test_parse_test_output_regex.py
@@ -0,0 +1,189 @@
+"""Tests for the regex patterns and string matching in parse_test_output.py."""
+
+from codeflash.verification.parse_test_output import (
+    matches_re_end,
+    matches_re_start,
+    parse_test_failures_from_stdout,
+)
+
+
+# --- matches_re_start tests ---
+
+
+class TestMatchesReStart:
+    def test_simple_no_class(self) -> None:
+        s = "!$######tests.test_foo:test_bar:target_func:1:abc######$!\n"
+        m = matches_re_start.search(s)
+        assert m is not None
+        assert m.groups() == ("tests.test_foo", "", "test_bar", "target_func", "1", "abc")
+
+    def test_with_class(self) -> None:
+        s = "!$######tests.test_foo:MyClass.test_bar:target_func:1:abc######$!\n"
+        m = matches_re_start.search(s)
+        assert m is not None
+        assert m.groups() == ("tests.test_foo", "MyClass.", "test_bar", "target_func", "1", "abc")
+
+    def test_nested_class(self) -> None:
+        s = "!$######a.b.c:A.B.test_x:func:3:id123######$!\n"
+        m = matches_re_start.search(s)
+        assert m is not None
+        assert m.groups() == ("a.b.c", "A.B.", "test_x", "func", "3", "id123")
+
+    def test_empty_class_and_function(self) -> None:
+        s = "!$######mod::func:0:iter######$!\n"
+        m = matches_re_start.search(s)
+        assert m is not None
+        assert m.groups() == ("mod", "", "", "func", "0", "iter")
+
+    def test_embedded_in_stdout(self) -> None:
+        s = "some output\n!$######mod:test_fn:f:1:x######$!\nmore output\n"
+        m = matches_re_start.search(s)
+        assert m is not None
+        assert m.groups() == ("mod", "", "test_fn", "f", "1", "x")
+
+    def test_multiple_matches(self) -> None:
+        s = (
+            "!$######m1:C1.fn1:t1:1:a######$!\n"
+            "!$######m2:fn2:t2:2:b######$!\n"
+        )
+        matches = list(matches_re_start.finditer(s))
+        assert len(matches) == 2
+        assert matches[0].groups() == ("m1", "C1.", "fn1", "t1", "1", "a")
+        assert matches[1].groups() == ("m2", "", "fn2", "t2", "2", "b")
+
+    def test_no_match_without_newline(self) -> None:
+        s = "!$######mod:test_fn:f:1:x######$!"
+        m = matches_re_start.search(s)
+        assert m is None
+
+    def test_dots_in_module_path(self) -> None:
+        s = "!$######a.b.c.d.e:test_fn:f:1:x######$!\n"
+        m = matches_re_start.search(s)
+        assert m is not None
+        assert m.group(1) == "a.b.c.d.e"
+
+
+# --- matches_re_end tests ---
+
+
+class TestMatchesReEnd:
+    def test_simple_no_class_with_runtime(self) -> None:
+        s = "!######tests.test_foo:test_bar:target_func:1:abc:12345######!"
+        m = matches_re_end.search(s)
+        assert m is not None
+        assert m.groups() == ("tests.test_foo", "", "test_bar", "target_func", "1", "abc:12345")
+
+    def test_with_class_no_runtime(self) -> None:
+        s = "!######tests.test_foo:MyClass.test_bar:target_func:1:abc######!"
+        m = matches_re_end.search(s)
+        assert m is not None
+        assert m.groups() == ("tests.test_foo", "MyClass.", "test_bar", "target_func", "1", "abc")
+
+    def test_nested_class_with_runtime(self) -> None:
+        s = "!######mod:A.B.test_x:func:3:id123:99999######!"
+        m = matches_re_end.search(s)
+        assert m is not None
+        assert m.groups() == ("mod", "A.B.", "test_x", "func", "3", "id123:99999")
+
+    def test_runtime_colon_preserved_in_group6(self) -> None:
+        """Group 6 must capture 'iteration_id:runtime' as a single string (colon included)."""
+        s = "!######m:fn:f:1:iter42:98765######!"
+        m = matches_re_end.search(s)
+        assert m is not None
+        assert m.group(6) == "iter42:98765"
+
+    def test_embedded_in_stdout(self) -> None:
+        s = "captured output\n!######mod:test_fn:f:1:x:500######!\nmore"
+        m = matches_re_end.search(s)
+        assert m is not None
+        assert m.groups() == ("mod", "", "test_fn", "f", "1", "x:500")
+
+
+# --- Start/End pairing (simulates parse_test_xml matching logic) ---
+
+
+class TestStartEndPairing:
+    def test_paired_markers(self) -> None:
+        stdout = (
+            "!$######mod:Class.test_fn:func:1:iter1######$!\n"
+            "test output here\n"
+            "!######mod:Class.test_fn:func:1:iter1:54321######!"
+        )
+        starts = list(matches_re_start.finditer(stdout))
+        ends = {}
+        for match in matches_re_end.finditer(stdout):
+            groups = match.groups()
+            g5 = groups[5]
+            colon_pos = g5.find(":")
+            if colon_pos != -1:
+                key = groups[:5] + (g5[:colon_pos],)
+            else:
+                key = groups
+            ends[key] = match
+
+        assert len(starts) == 1
+        assert len(ends) == 1
+        # Start and end should pair on the first 5 groups + iteration_id
+        start_groups = starts[0].groups()
+        assert start_groups in ends
+
+
+# --- parse_test_failures_from_stdout tests ---
+
+
+class TestParseTestFailuresHeader:
+    def test_standard_pytest_header(self) -> None:
+        stdout = (
+            "..F.\n"
+            "=================================== FAILURES ===================================\n"
+            "_______ test_foo _______\n"
+            "\n"
+            "    def test_foo():\n"
+            ">       assert False\n"
+            "E       AssertionError\n"
+            "\n"
+            "test.py:3: AssertionError\n"
+            "=========================== short test summary info ============================\n"
+            "FAILED test.py::test_foo\n"
+        )
+        result = parse_test_failures_from_stdout(stdout)
+        assert "test_foo" in result
+
+    def test_minimal_equals(self) -> None:
+        """Even a short '= FAILURES =' header should be detected."""
+        stdout = (
+            "= FAILURES =\n"
+            "_______ test_bar _______\n"
+            "\n"
+            "    assert False\n"
+            "\n"
+            "test.py:1: AssertionError\n"
+            "= short test summary info =\n"
+        )
+        result = parse_test_failures_from_stdout(stdout)
+        assert "test_bar" in result
+
+    def test_no_failures_section(self) -> None:
+        stdout = "....\n4 passed in 0.1s\n"
+        result = parse_test_failures_from_stdout(stdout)
+        assert result == {}
+
+    def test_word_failures_without_equals_is_not_matched(self) -> None:
+        """'FAILURES' without surrounding '=' signs should not trigger the header detection."""
+        stdout = (
+            "FAILURES detected in module\n"
+            "_______ test_baz _______\n"
+            "\n"
+            "    assert False\n"
+        )
+        result = parse_test_failures_from_stdout(stdout)
+        assert result == {}
+
+    def test_failures_in_test_output_not_matched(self) -> None:
+        """A test printing 'FAILURES' (no = signs) should not trigger header detection."""
+        stdout = (
+            "Testing FAILURES handling\n"
+            "All good\n"
+        )
+        result = parse_test_failures_from_stdout(stdout)
+        assert result == {}