fixes for broken tools, integrations tests, & docs

Fixes found by stress-testing MCP tools against real CodeQL databases:

- bqrs_decode: replace non-existent --max-results/--max-paths with correct
  --rows option; add --result-set, --entities, --sort-direction, --no-titles
- bqrs_info: add --format (text/json), --paginate-rows, --paginate-result-set;
  fix format passthrough in cli-tool-registry (formatShouldBePassedToCLI)
- list_query_run_results: add language/queryPath filters; extract metadata
  from query.log (queryPath, databasePath, language); add fallback language
  detection from semmlecode.<lang>.dbscheme and codeql/<lang>-all/ paths
- database_analyze: add --rerun parameter; auto-create output parent directory
  to prevent NoSuchFileException after long-running evaluations
- query_run: fix SARIF generation to use interpretBQRSFile with proper -t
  metadata instead of bare bqrs interpret; fix output filename to
  results-interpreted.sarif
- `docs/**/*.md`: update project docs to reflect ^ improvements to
  tools.

Unit tests: 873 passed (44 files, +23 new tests)
Integration tests: 5 new test cases covering each fix

Author: data-douser

client/integration-tests/primitives/tools/codeql_bqrs_decode/decode_with_result_set/README.md

@@ -0,0 +1,17 @@
+# `codeql_bqrs_decode` - decode_with_result_set
+
+## Purpose
+
+Tests the `codeql_bqrs_decode` tool with the `result-set` parameter to decode
+a specific result set from a BQRS file. This test exercises the `--result-set`,
+`--format`, and `--no-titles` CLI options which were previously untested,
+allowing non-existent options like `--max-results` to go undetected.
+
+## Inputs
+
+- `before/results.bqrs` — BQRS file with a `#select` result set (1 row, 2 columns).
+- `test-config.json` — Specifies `result-set`, `format`, and `no-titles` arguments.
+
+## Outputs
+
+- Tool returns decoded CSV output for the `#select` result set without column headers.

client/integration-tests/primitives/tools/codeql_bqrs_decode/decode_with_result_set/after/monitoring-state.json

@@ -0,0 +1,14 @@
+{
+  "sessions": [
+    {
+      "id": "integration_test_session",
+      "calls": [
+        {
+          "tool": "codeql_bqrs_decode",
+          "timestamp": "2025-09-25T16:06:00.000Z",
+          "status": "success"
+        }
+      ]
+    }
+  ]
+}

client/integration-tests/primitives/tools/codeql_bqrs_decode/decode_with_result_set/before/monitoring-state.json

@@ -0,0 +1,3 @@
+{
+  "sessions": []
+}

client/integration-tests/primitives/tools/codeql_bqrs_decode/decode_with_result_set/before/results.bqrs

@@ -0,0 +1,9 @@
+{
+  "toolName": "codeql_bqrs_decode",
+  "arguments": {
+    "files": ["client/integration-tests/primitives/tools/codeql_bqrs_decode/decode_with_result_set/before/results.bqrs"],
+    "format": "csv",
+    "result-set": "#select",
+    "no-titles": true
+  }
+}

client/integration-tests/primitives/tools/codeql_bqrs_decode/decode_with_result_set/test-config.json

@@ -0,0 +1,9 @@
+# `codeql_bqrs_info` - json_format
+
+## Purpose
+
+Tests the `codeql_bqrs_info` tool with `format=json` to get machine-readable
+output. This test exercises the `--format` CLI option being passed through to
+the CLI correctly — previously `format` was silently swallowed by the tool
+registry and not passed to `codeql bqrs info`, causing quiet fallback to text
+format.

client/integration-tests/primitives/tools/codeql_bqrs_info/json_format/README.md

@@ -0,0 +1,14 @@
+{
+  "sessions": [
+    {
+      "id": "integration_test_session",
+      "calls": [
+        {
+          "tool": "codeql_bqrs_info",
+          "timestamp": "2025-09-25T16:06:00.000Z",
+          "status": "success"
+        }
+      ]
+    }
+  ]
+}

client/integration-tests/primitives/tools/codeql_bqrs_info/json_format/after/monitoring-state.json

@@ -0,0 +1,3 @@
+{
+  "sessions": []
+}

client/integration-tests/primitives/tools/codeql_bqrs_info/json_format/before/monitoring-state.json

@@ -0,0 +1,7 @@
+{
+  "toolName": "codeql_bqrs_info",
+  "arguments": {
+    "files": ["client/integration-tests/primitives/tools/codeql_bqrs_info/json_format/before/results.bqrs"],
+    "format": "json"
+  }
+}