Fix CLI overrides LogLevel value from config file (#3426)

## Why make this change?
- Closes issue #3258
Whenever we use the `dab start` command the CLI overrides the minimum
LogLevel from the configuration file. This is acceptable only if we use
the `--LogLevel` flag. If we do not use that flag, the LogLevel for each
namespace should be decided by the configuration file.

## What is this change?
This change moves the `args.Add` methods inside the `ConfigGenerator.cs`
so that they are only applied when we use the `--LogLevel` flag. Having
these arguments causes DAB to not allow any changes to the LogLevel in
the loggers, since those arguments were always being added, DAB always
assumed the CLI was overriding the LogLevel when it was not expected as
it would use the `--LogLevel` flag to determine if it was an
`IsLogLevelOverridenByCli` scenario.

## How was this tested?

- [ ] Integration Tests
- [x] Unit Tests
- [x] Manual Tests
Tested with different configurations of the namespaces in the
`log-level` property inside the config file.
Note: ALL these manual tests were tested by running the CLI as well as
running DAB through Visual Studio.
Config file includes:
```
"log-level": {
    "Azure.DataApiBuilder.Core.Services.ISqlMetadataProvider": "Information",
    "Azure.DataApiBuilder.Core": "Debug",
    "Azure.DataApiBuilder.Config.FileSystemRuntimeConfigLoader": "Error",
    "default": "Warning"
}
```
Expected results:
- All the logs from
`Azure.DataApiBuilder.Core.Services.ISqlMetadataProvider` will provide
logs from log level information and above.
- All logs from `Azure.DataApiBuilder.Core` and its sub-namespaces that
are not from `ISqlMetadataProvider` will provide logs from log level
debug and above.
- All logs from
`Azure.DataApiBuilder.Config.FileSystemRuntimeConfigLoader` will provide
logs from log level error and above.
- Everything else will provide logs from log level warning and above,
including CLI.

Config file includes:
```
"log-level": {
    "Azure.DataApiBuilder.Core": "Information",
    "Azure.DataApiBuilder.Config": "Debug",
}
```
Expected results:
- All logs from `Azure.DataApiBuilder.Core` and its sub-namespaces will
provide logs from log level information and above.
- All logs from `Azure.DataApiBuilder.Config` and its sub-namespaces
will provide logs from log level debug and above.
- Everything else will provide logs from log level debug and above with
`host.mode = development`, including CLI.

Config file includes:
```
"log-level": {
    "Default: none
}
```
Expected results:
- No logs will be printed, including CLI.

## Sample Request(s)
dab start --LogLevel information

dab start (With config file default value debug)

Author: RubenCerna2079

src/Cli.Tests/EndToEndTests.cs

@@ -3,6 +3,7 @@
 
 using Azure.DataApiBuilder.Config.Converters;
 using Azure.DataApiBuilder.Product;
+using Azure.DataApiBuilder.Service;
 using Cli.Constants;
 using Microsoft.Data.SqlClient;
 
@@ -857,6 +858,83 @@ public void TestEngineStartUpWithVerboseAndLogLevelOptions(string logLevelOption
         StringAssert.Contains(output, $"User provided config file: {TEST_RUNTIME_CONFIG_FILE}", StringComparison.Ordinal);
     }
 
+    /// <summary>
+    /// Validates that `dab start` correctly sets <see cref="Startup.IsLogLevelOverriddenByCli"/>
+    /// based on whether the --LogLevel CLI flag is provided.
+    ///
+    /// When the --LogLevel flag is provided, IsLogLevelOverriddenByCli should be true.
+    /// When the --LogLevel flag is omitted (log level comes from the config file), IsLogLevelOverriddenByCli should be false.
+    /// </summary>
+    /// <param name="cliLogLevel">The --LogLevel CLI flag value, or null to omit the flag.</param>
+    /// <param name="expectedIsOverridden">Expected value of Startup.IsLogLevelOverriddenByCli.</param>
+    [DataTestMethod]
+    [DataRow(null, false, DisplayName = "IsLogLevelOverriddenByCli is false")]
+    [DataRow(LogLevel.Error, true, DisplayName = "IsLogLevelOverriddenByCli is true")]
+    public async Task TestStartCommandResolvesLogLevelFromConfigOrFlag(
+        LogLevel? cliLogLevel,
+        bool expectedIsOverridden)
+    {
+        string baseConfig = @"
+        {
+            ""$schema"": """ + DAB_DRAFT_SCHEMA_TEST_PATH + @""",
+            ""data-source"": {
+                ""database-type"": ""mssql"",
+                ""connection-string"": """ + SAMPLE_TEST_CONN_STRING + @"""
+            },
+            ""runtime"": {
+                ""rest"": {
+                    ""path"": ""/api"",
+                    ""enabled"": true
+                },
+                ""graphql"": {
+                    ""path"": ""/graphql"",
+                    ""enabled"": true,
+                    ""allow-introspection"": true
+                },
+                ""host"": {
+                    ""mode"": ""development"",
+                    ""cors"": {
+                        ""origins"": [],
+                        ""allow-credentials"": false
+                    },
+                    ""authentication"": {
+                        ""provider"": ""Unauthenticated""
+                    }
+                },
+                ""telemetry"": {
+                    ""log-level"": {
+                        ""Azure.DataApiBuilder.Core.Services.ISqlMetadataProvider"": ""Information"",
+                        ""Azure.DataApiBuilder.Core"": ""Debug"",
+                        ""Azure.DataApiBuilder.Service.Controllers.RestController"": ""Error"",
+                        ""default"": ""Warning""
+                    }
+                }
+            },
+            ""entities"": {}
+        }";
+
+        // Merge in an entity so the config is not rejected for having an empty entities section.
+        string configWithLogLevel = AddPropertiesToJson(baseConfig, BASIC_ENTITY_WITH_ANONYMOUS_ROLE);
+        _fileSystem!.File.WriteAllText(TEST_RUNTIME_CONFIG_FILE, configWithLogLevel);
+
+        StartOptions options = new(
+            verbose: false,
+            logLevel: cliLogLevel,
+            isHttpsRedirectionDisabled: false,
+            mcpStdio: false,
+            mcpRole: null,
+            config: TEST_RUNTIME_CONFIG_FILE);
+
+        // Run TryStartEngineWithOptions on a background task because StartEngine blocks until the host shuts down.
+        Task engineTask = Task.Run(() =>
+            TryStartEngineWithOptions(options, _runtimeConfigLoader!, _fileSystem!));
+
+        // Wait for the engine to finish loading the config.
+        await Task.Delay(TimeSpan.FromSeconds(5));
+
+        Assert.AreEqual(expectedIsOverridden, Startup.IsLogLevelOverriddenByCli);
+    }
+
     /// <summary>
     /// Validates that valid usage of verbs and associated options produce exit code 0 (CliReturnCode.SUCCESS).
     /// Verifies that explicitly implemented verbs (add, update, init, start) and appropriately

src/Cli/ConfigGenerator.cs

@@ -2732,18 +2732,10 @@ public static bool TryStartEngineWithOptions(StartOptions options, FileSystemRun
                 }
 
                 minimumLogLevel = (LogLevel)options.LogLevel;
+                args.Add("--LogLevel");
+                args.Add(minimumLogLevel.ToString());
                 _logger.LogInformation("Setting minimum LogLevel: {minimumLogLevel}.", minimumLogLevel);
             }
-            else
-            {
-                minimumLogLevel = deserializedRuntimeConfig.GetConfiguredLogLevel();
-                HostMode hostModeType = deserializedRuntimeConfig.IsDevelopmentMode() ? HostMode.Development : HostMode.Production;
-
-                _logger.LogInformation($"Setting default minimum LogLevel: {minimumLogLevel} for {hostModeType} mode.", minimumLogLevel, hostModeType);
-            }
-
-            args.Add("--LogLevel");
-            args.Add(minimumLogLevel.ToString());
 
             // This will add args to disable automatic redirects to https if specified by user
             if (options.IsHttpsRedirectionDisabled)