diff --git a/compose.yaml b/compose.yaml
index 0d0d05a7..f5ebb527 100644
--- a/compose.yaml
+++ b/compose.yaml
@@ -4,7 +4,8 @@ x-common-variables: &kai-variables
   DEMO_MODE: "False"
   HUB_URL: ${HUB_URL:-https://tackle-konveyor-tackle.apps.example.com/hub}
   IMPORTER_ARGS:
-  LOGLEVEL: info
+  LOG_LEVEL: info
+  LOG_DIR: "/podman_compose/logs"
   NUM_WORKERS: 8
   USE_HUB_IMPORTER: ${USE_HUB_IMPORTER:-False}
 
@@ -27,7 +28,7 @@ services:
       OPENAI_API_KEY:
     image: ${IMAGE:-quay.io/konveyor/kai}:${TAG:-stable}
     volumes:
-      - ${PWD}:/podman_compose:ro,z
+      - ${PWD}:/podman_compose:rw,z
     ports:
       - "8080:8080"
     depends_on:
@@ -39,7 +40,7 @@ services:
       MODE: importer
     image: ${IMAGE:-quay.io/konveyor/kai}:${TAG:-stable}
     volumes:
-      - ${PWD}:/podman_compose:ro,z
+      - ${PWD}:/podman_compose:rw,z
     depends_on:
       - kai_db
     profiles:
diff --git a/example/run_demo.py b/example/run_demo.py
index 59bf2c37..bf313643 100755
--- a/example/run_demo.py
+++ b/example/run_demo.py
@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 
 import json
+import logging
 import os
 import sys
 import time
@@ -12,8 +13,10 @@
 
 # Ensure that we have 'kai' in our import path
 sys.path.append("../../kai")
-from kai import Report
-from kai.kai_logging import KAI_LOG
+from kai.kai_logging import formatter
+from kai.report import Report
+
+KAI_LOG = logging.getLogger(__name__)
 
 SERVER_URL = "http://0.0.0.0:8080"
 APP_NAME = "coolstore"
@@ -249,7 +252,11 @@ def run_demo(report):
 
 
 if __name__ == "__main__":
-    KAI_LOG.setLevel("info".upper())
+    console_handler = logging.StreamHandler()
+    console_handler.setFormatter(formatter)
+    KAI_LOG.addHandler(console_handler)
+    KAI_LOG.setLevel("DEBUG")
+
     start = time.time()
     coolstore_analysis_dir = "./analysis/coolstore/output.yaml"
     r = Report.load_report_from_file(coolstore_analysis_dir)
diff --git a/kai/__init__.py b/kai/__init__.py
index 650f3222..f102a9ca 100644
--- a/kai/__init__.py
+++ b/kai/__init__.py
@@ -1,120 +1 @@
 __version__ = "0.0.1"
-
-from typing import Annotated, List
-
-import typer
-
-from kai.report import Report
-from kai.result import LLMResult
-from kai.service.incident_store.incident_store import IncidentStore
-
-# from typing_extensions import Annotated
-
-
-app = typer.Typer()
-
-# report_app = typer.Typer()
-# result_app = typer.Typer()
-
-# app.add_typer(report_app, name="report", help="Generate a markdown report from a raw analysis yaml.")
-# app.add_typer(result_app, name="result", help="Generate patches for given violations and incidents from an analysis yaml")
-
-
-@app.command()
-def report(analysis_path: str, output_dir: str):
-    """
-    Generate a Markdown report of a given analysis
-    YAML to be read by a human
-    """
-    report = Report.load_report_from_file(analysis_path)
-    r = dict(report)
-    print(f"We have results from {len(r.keys())} RuleSet(s) in {analysis_path}\n")
-    report.write_markdown(output_dir)
-
-
-@app.command()
-def generate(
-    path_to_report: str,
-    path_to_source: str,
-    example_initial_branch: str,
-    example_solved_branch: str,
-    path_to_output: str,
-    limit_rulesets: Annotated[List[str], typer.Option("--ruleset", "-r")] = None,
-    limit_violations: Annotated[List[str], typer.Option("--violation", "-v")] = None,
-    model: Annotated[str, typer.Option("--model", "-m")] = "gpt-3.5-turbo-16k",
-):
-    # model: Annotated[Optional[str], typer.Argument()] = "gpt-3.5-turbo-16k"):
-    """
-    Generate patches for given violations and incidents from an analysis yaml report
-
-    - path_to_report: Path to the analysis yaml report
-
-    - path_to_source: Path to the source code to be patched
-
-    - example_initial_branch: Branch name for the initial state of the source code
-
-    - example_solved_branch: Branch name for the solved state of the source code
-
-    - path_to_output: Path to the output directory for the patches
-
-    - limit_rulesets: Limit to specific rulesets (defaults to 'None', meaning to run all)
-
-    - limit_violations: Limit to specific violations (defaults to 'None', meaning to run all)
-
-    - model: Model name to use for generating the patches (defaults to 'gpt-3.5-turbo-16k', 'gpt-4-1106-preview' is another good option)
-    """
-    print(
-        f"Generating patches for {path_to_report} for example app at {path_to_source}"
-    )
-    print(f"Initial branch: {example_initial_branch}")
-    print(f"Solved branch: {example_solved_branch}")
-    print(f"Output directory: {path_to_output}")
-    print(f"Model: {model}")
-    print(f"Limit to ruleset(s): {limit_rulesets}")
-    print(f"Limit to violation(s): {limit_violations}")
-
-    llmResult = LLMResult(path_to_source, example_initial_branch, example_solved_branch)
-    llmResult.parse_report(path_to_report)
-    llmResult.process(path_to_output, model, limit_rulesets, limit_violations)
-    print(f"Completed processing, output written to {path_to_output}\n")
-
-
-@app.command()
-def load(report_path: str, output_dir: str):
-    """
-    Load the incident store with the given applications
-    write the cached_violations to a file for later use
-    """
-    incident_store = IncidentStore(report_path, output_dir)
-    incident_store.load_incident_store()
-
-
-@app.command()
-def patch(ruleset: str, violation: str, report_path: str, output_dir: str):
-    """
-    Generate patches for a specific violation
-    """
-    print(f"Generating patches for {ruleset} - {violation}")
-    incident_store = IncidentStore(report_path, output_dir)
-    patches = incident_store.get_solved_issue(ruleset, violation)
-    if len(patches) == 0:
-        print(f"No patches found for {ruleset} - {violation}")
-    else:
-        for patch in patches:
-            print(f"Patch: {patch}")
-    return patches
-
-
-@app.command()
-def common(ruleset: str, violation: str, report_path: str, output_dir: str):
-    """
-    Find common violations for a specific violation
-    """
-    print(f"Finding common violations for {ruleset} - {violation}")
-    incident_store = IncidentStore(report_path, output_dir)
-    violations = incident_store.find_common_violations(ruleset, violation)
-    if violations is None:
-        print(f"No common violations found for {ruleset} - {violation}")
-    for violation in violations:
-        print(f"Violation: {violation}")
-    return violations
diff --git a/kai/config.toml b/kai/config.toml
index f507822e..16227cf3 100644
--- a/kai/config.toml
+++ b/kai/config.toml
@@ -1,4 +1,6 @@
 log_level = "info"
+file_log_level = "debug"
+log_dir = "$pwd/logs"
 demo_mode = false
 trace_enabled = true
 
diff --git a/kai/embedding_provider.py b/kai/embedding_provider.py
index 9c424d26..44b9d915 100644
--- a/kai/embedding_provider.py
+++ b/kai/embedding_provider.py
@@ -1,3 +1,4 @@
+import logging
 import random
 from abc import ABC, abstractmethod
 from enum import Enum
@@ -9,7 +10,7 @@
 from psycopg2 import sql
 from psycopg2.extensions import connection
 
-from kai.kai_logging import KAI_LOG
+KAI_LOG = logging.getLogger(__name__)
 
 
 class TrimStrategy(Enum):
diff --git a/kai/hub_importer.py b/kai/hub_importer.py
index 927dcce1..288aeb74 100755
--- a/kai/hub_importer.py
+++ b/kai/hub_importer.py
@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 
 import argparse
+import logging
 import os
 import pprint
 import tempfile
@@ -13,11 +14,12 @@
 from git import GitCommandError, Repo
 from pydantic import BaseModel, Field
 
-from kai.kai_logging import KAI_LOG
 from kai.models.kai_config import KaiConfig
 from kai.report import Report
 from kai.service.incident_store import Application, IncidentStore
 
+KAI_LOG = logging.getLogger(__name__)
+
 
 # BaseModel that also acts as a dict
 class KaiBaseModel(BaseModel):
diff --git a/kai/kai_logging.py b/kai/kai_logging.py
index 9a8ca961..9ebfa131 100644
--- a/kai/kai_logging.py
+++ b/kai/kai_logging.py
@@ -1,10 +1,63 @@
 import logging
+import os
 
-KAI_LOG = logging.getLogger(__name__)
-console_handler = logging.StreamHandler()
+from kai.models.kai_config import KaiConfig
+
+parent_log = logging.getLogger("kai")
+
+# console_handler = logging.StreamHandler()
 # formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
 formatter = logging.Formatter(
-    "%(levelname)s - %(asctime)s - [%(filename)20s:%(lineno)-4s - %(funcName)20s()] - %(message)s"
+    "%(levelname)s - %(asctime)s - %(name)s - [%(filename)20s:%(lineno)-4s - %(funcName)20s()] - %(message)s"
 )
-console_handler.setFormatter(formatter)
-KAI_LOG.addHandler(console_handler)
+
+
+def process_log_dir_replacements(log_dir: str):
+    ##
+    # We want to replace $pwd with the location of the Kai project directory,
+    # this is needed to help with specifying from configuration
+    ##
+    if log_dir.startswith("$pwd"):
+        log_dir = log_dir.replace(
+            "$pwd", os.path.join(os.path.dirname(os.path.realpath(__file__)), "../")
+        )
+    return log_dir
+
+
+def setup_console_handler(logger, log_level: str = "INFO"):
+    console_handler = logging.StreamHandler()
+    console_handler.setLevel(log_level)
+    console_handler.setFormatter(formatter)
+    logger.addHandler(console_handler)
+    print(f"Console logging for '{parent_log.name}' is set to level '{log_level}'")
+
+
+def setup_file_handler(
+    logger, log_file_name: str, log_dir: str, log_level: str = "DEBUG"
+):
+    # Ensure any needed log directories exist
+    log_dir = process_log_dir_replacements(log_dir)
+    log_file_path = os.path.join(log_dir, log_file_name)
+    if log_dir.startswith("$pwd"):
+        log_dir = os.path.join(os.getcwd(), log_dir[5:])
+    os.makedirs(os.path.dirname(log_file_path), exist_ok=True)
+
+    file_handler = logging.FileHandler(log_file_path)
+    file_handler.setLevel(log_level)
+    file_handler.setFormatter(formatter)
+    logger.addHandler(file_handler)
+    print(
+        f"File logging for '{logger.name}' is set to level '{log_level}' writing to file: '{log_file_path}'"
+    )
+
+
+def initLogging(console_log_level, file_log_level, log_dir, log_file="kai_server.log"):
+    setup_console_handler(parent_log, console_log_level)
+    setup_file_handler(parent_log, log_file, log_dir, file_log_level)
+    # Attempt to set the parent log level to
+    # most persmissive and allow child loggers to control what is filtered or not
+    parent_log.setLevel("DEBUG")
+
+
+def initLoggingFromConfig(config: KaiConfig):
+    initLogging(config.log_level.upper(), config.file_log_level.upper(), config.log_dir)
diff --git a/kai/llm_io_handler.py b/kai/llm_io_handler.py
index f6b4d824..12e06ef3 100644
--- a/kai/llm_io_handler.py
+++ b/kai/llm_io_handler.py
@@ -1,4 +1,5 @@
 import itertools
+import logging
 import os
 import time
 import traceback
@@ -16,7 +17,6 @@
 )
 
 from kai.constants import PATH_TEMPLATES
-from kai.kai_logging import KAI_LOG
 from kai.model_provider import ModelProvider
 from kai.models.file_solution import guess_language, parse_file_solution_content
 from kai.service.incident_store.incident_store import IncidentStore
@@ -25,6 +25,8 @@
 LLM_RETRIES = 5
 LLM_RETRY_DELAY = 10
 
+KAI_LOG = logging.getLogger(__name__)
+
 
 def get_prompt(
     model_provider: ModelProvider,
diff --git a/kai/models/file_solution.py b/kai/models/file_solution.py
index 51b5c867..3e27e089 100644
--- a/kai/models/file_solution.py
+++ b/kai/models/file_solution.py
@@ -1,10 +1,11 @@
+import logging
 import re
 
 from pydantic import BaseModel
 from pygments import lexers
 from pygments.util import ClassNotFound
 
-from kai.kai_logging import KAI_LOG
+KAI_LOG = logging.getLogger(__name__)
 
 
 class FileSolutionContent(BaseModel):
diff --git a/kai/models/kai_config.py b/kai/models/kai_config.py
index ab606842..a6166e36 100644
--- a/kai/models/kai_config.py
+++ b/kai/models/kai_config.py
@@ -92,6 +92,10 @@ class KaiConfigModels(BaseModel):
 
 class KaiConfig(BaseModel):
     log_level: str = "info"
+    file_log_level: str = "info"
+    log_dir: str = os.path.join(
+        os.path.dirname(os.path.realpath(__file__)), "../../logs"
+    )
     demo_mode: bool = False
     trace_enabled: bool = False
 
diff --git a/kai/report.py b/kai/report.py
index 7383b5cd..9ee01f8d 100644
--- a/kai/report.py
+++ b/kai/report.py
@@ -2,13 +2,14 @@
 
 import hashlib
 import json
+import logging
 import os
 import shutil
 from io import StringIO
 
 import yaml
 
-from kai.kai_logging import KAI_LOG
+KAI_LOG = logging.getLogger(__name__)
 
 
 class Report:
diff --git a/kai/result.py b/kai/result.py
index a1bd792e..a2547e01 100644
--- a/kai/result.py
+++ b/kai/result.py
@@ -1,5 +1,6 @@
 __all__ = ["LLMResult"]
 
+import logging
 import os
 
 from langchain.chains import LLMChain
@@ -7,11 +8,12 @@
 from langchain_community.chat_models import ChatOpenAI
 
 from kai.constants import PATH_TEMPLATES
-from kai.kai_logging import KAI_LOG
 
 from .report import Report
 from .scm import GitDiff
 
+KAI_LOG = logging.getLogger(__name__)
+
 
 class LLMResult:
     """The intent of this class is to help us form several Prompt examples using a single application
diff --git a/kai/scm.py b/kai/scm.py
index fbd7d7c2..5921c365 100644
--- a/kai/scm.py
+++ b/kai/scm.py
@@ -1,9 +1,10 @@
 __all__ = ["GitDiff"]
 
+import logging
 
 from git import BadName, Repo
 
-from kai.kai_logging import KAI_LOG
+KAI_LOG = logging.getLogger(__name__)
 
 
 class GitDiff:
diff --git a/kai/server.py b/kai/server.py
index d5db510f..6dc3d846 100644
--- a/kai/server.py
+++ b/kai/server.py
@@ -5,6 +5,7 @@
 import argparse
 import datetime
 import json
+import logging
 import os
 import pprint
 import time
@@ -19,13 +20,15 @@
 
 from kai import llm_io_handler
 from kai.constants import PATH_KAI
-from kai.kai_logging import KAI_LOG
+from kai.kai_logging import initLoggingFromConfig
 from kai.model_provider import ModelProvider
 from kai.models.analyzer_types import Incident
 from kai.models.kai_config import KaiConfig
 from kai.report import Report
 from kai.service.incident_store.incident_store import Application, IncidentStore
 
+log = logging.getLogger(__name__)
+
 # TODO: Make openapi spec for everything
 
 # TODO: Repo lives both on client and on server. Determine either A) Best way to
@@ -45,7 +48,7 @@
 
 @routes.post("/health_check")
 async def post_dummy_json_request(request: Request):
-    KAI_LOG.debug(f"health_check recv'd: {request}")
+    log.debug(f"health_check recv'd: {request}")
 
     request_json: dict = await request.json()
 
@@ -112,7 +115,7 @@ async def post_get_incident_solution(request: Request):
     Stateful, stores it
     """
 
-    KAI_LOG.debug(f"post_get_incident_solution recv'd: {request}")
+    log.debug(f"post_get_incident_solution recv'd: {request}")
 
     params = PostGetIncidentSolutionParams.model_validate(await request.json())
 
@@ -210,10 +213,10 @@ class PostGetIncidentSolutionsForFileParams(BaseModel):
 @routes.post("/get_incident_solutions_for_file")
 async def get_incident_solutions_for_file(request: Request):
     start = time.time()
-    KAI_LOG.debug(f"get_incident_solutions_for_file recv'd: {request}")
+    log.debug(f"get_incident_solutions_for_file recv'd: {request}")
     params = PostGetIncidentSolutionsForFileParams.model_validate(await request.json())
 
-    KAI_LOG.info(
+    log.info(
         f"START - App: '{params.application_name}', File: '{params.file_name}' with {len(params.incidents)} incidents'"
     )
 
@@ -247,7 +250,7 @@ async def get_incident_solutions_for_file(request: Request):
     finally:
         end = time.time()
         trace.end(end)
-        KAI_LOG.info(
+        log.info(
             f"END - completed in '{end-start}s:  - App: '{params.application_name}', File: '{params.file_name}' with {len(params.incidents)} incidents'"
         )
 
@@ -271,38 +274,38 @@ def app():
     else:
         raise FileNotFoundError("Config file not found.")
 
-    if os.getenv("LOGLEVEL") is not None:
-        config.log_level = os.getenv("LOGLEVEL").upper()
+    if os.getenv("LOG_LEVEL") is not None:
+        config.log_level = os.getenv("LOG_LEVEL").upper()
     if os.getenv("DEMO_MODE") is not None:
         config.demo_mode = os.getenv("DEMO_MODE").lower() == "true"
     if os.getenv("TRACE") is not None:
         config.trace_enabled = os.getenv("TRACE").lower() == "true"
+    if os.getenv("LOG_DIR") is not None:
+        config.log_dir = os.getenv("LOG_DIR")
 
     print(f"Config loaded: {pprint.pformat(config)}")
-
-    config: KaiConfig
     webapp["config"] = config
+    initLoggingFromConfig(config)
 
-    KAI_LOG.setLevel(config.log_level.upper())
     print(
         f"Logging for KAI has been initialized and the level set to {config.log_level.upper()}"
     )
 
-    KAI_LOG.info(
+    log.info(
         f"Tracing of actions is {'enabled' if config.trace_enabled else 'disabled'}"
     )
 
     if config.demo_mode:
-        KAI_LOG.info("DEMO_MODE is enabled. LLM responses will be cached")
+        log.info("DEMO_MODE is enabled. LLM responses will be cached")
 
     webapp["model_provider"] = ModelProvider(config.models)
-    KAI_LOG.info(f"Selected provider: {config.models.provider}")
-    KAI_LOG.info(f"Selected model: {webapp['model_provider'].model_id}")
+    log.info(f"Selected provider: {config.models.provider}")
+    log.info(f"Selected model: {webapp['model_provider'].model_id}")
 
     webapp["incident_store"] = IncidentStore.from_config(
         config.incident_store, webapp["model_provider"]
     )
-    KAI_LOG.info(f"Selected incident store: {config.incident_store.provider}")
+    log.info(f"Selected incident store: {config.incident_store.provider}")
 
     webapp.add_routes(routes)
 
@@ -315,7 +318,7 @@ def main():
     arg_parser.add_argument(
         "-log",
         "--loglevel",
-        default=os.getenv("KAI_LOG_LEVEL", "info"),
+        default=os.getenv("LOG_LEVEL", "info"),
         choices=["debug", "info", "warning", "error", "critical"],
         help="""Provide logging level.
 Options:
@@ -336,7 +339,7 @@ def main():
 
     args, _ = arg_parser.parse_known_args()
 
-    os.environ["LOGLEVEL"] = str(args.loglevel)
+    os.environ["LOG_LEVEL"] = str(args.loglevel)
     os.environ["DEMO_MODE"] = str(args.demo_mode).lower()
 
     web.run_app(app())
diff --git a/kai/service/incident_store/incident_store.py b/kai/service/incident_store/incident_store.py
index 66de755e..3c0e0ed5 100644
--- a/kai/service/incident_store/incident_store.py
+++ b/kai/service/incident_store/incident_store.py
@@ -1,6 +1,7 @@
 import argparse
 import datetime
 import enum
+import logging
 import os
 from abc import ABC, abstractmethod
 from dataclasses import dataclass
@@ -24,7 +25,6 @@
 from sqlalchemy.types import JSON
 
 from kai.constants import PATH_LOCAL_REPO
-from kai.kai_logging import KAI_LOG
 from kai.model_provider import ModelProvider
 from kai.models.kai_config import (
     KaiConfig,
@@ -33,6 +33,8 @@
 )
 from kai.report import Report
 
+KAI_LOG = logging.getLogger(__name__)
+
 # These prefixes are sometimes in front of the paths, strip them.
 # Also strip leading slashes since os.path.join can't join two absolute paths
 KNOWN_PREFIXES = (
diff --git a/kai/service/incident_store/psql.py b/kai/service/incident_store/psql.py
index 5744d693..e3ca07ea 100644
--- a/kai/service/incident_store/psql.py
+++ b/kai/service/incident_store/psql.py
@@ -1,5 +1,8 @@
+import os
+
 from sqlalchemy import and_, create_engine
 
+from kai.kai_logging import initLogging
 from kai.model_provider import ModelProvider
 from kai.models.kai_config import KaiConfigIncidentStorePostgreSQLArgs
 from kai.service.incident_store.incident_store import IncidentStore, SQLIncident, cmd
@@ -27,4 +30,18 @@ def json_exactly_equal(self, json_dict: dict):
 
 
 if __name__ == "__main__":
+    if os.getenv("LOG_DIR") is not None:
+        log_dir = os.getenv("LOG_DIR")
+    else:
+        log_dir = os.path.join(
+            os.path.dirname(os.path.realpath(__file__)), "../../../logs"
+        )
+
+    if os.getenv("LOG_LEVEL") is not None:
+        log_level = os.getenv("LOG_LEVEL").upper()
+    else:
+        log_level = "INFO"
+
+    initLogging(log_level, "DEBUG", log_dir, "kai_psql.log")
+
     cmd("postgresql")
diff --git a/samples/fetch_apps.py b/samples/fetch_apps.py
index 68e5bd8d..4df3ab92 100755
--- a/samples/fetch_apps.py
+++ b/samples/fetch_apps.py
@@ -12,9 +12,8 @@ def fetch_sample_apps():
     for repo in repos:
         print(f"Cloning {repo}...")
         if os.path.exists(f"sample_repos/{repo}"):
-            print(f"*** Exiting since 'sample_repos/{repo}' already exists")
-            print("*** Delete 'sample_repos' and rerun this script")
-            sys.exit(1)
+            print(f"*** Skipping since 'sample_repos/{repo}' already exists")
+            continue
         gitCloneStatus = subprocess.run(  # trunk-ignore(bandit)
             ["git", "clone", repos[repo][0], f"sample_repos/{repo}"]
         )