java-codebase-rag 0.9.4__tar.gz → 0.9.6__tar.gz

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Files changed (134) hide show
  1. {java_codebase_rag-0.9.4/java_codebase_rag.egg-info → java_codebase_rag-0.9.6}/PKG-INFO +2 -2
  2. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6}/README.md +1 -1
  3. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6}/pyproject.toml +7 -25
  4. java_codebase_rag-0.9.6/src/java_codebase_rag/absence/__init__.py +0 -0
  5. java_codebase_rag-0.9.6/src/java_codebase_rag/absence/absence_diagnosis.py +700 -0
  6. java_codebase_rag-0.9.6/src/java_codebase_rag/absence/absence_types.py +124 -0
  7. java_codebase_rag-0.9.6/src/java_codebase_rag/absence/absence_vocab.py +455 -0
  8. java_codebase_rag-0.9.6/src/java_codebase_rag/analysis/__init__.py +0 -0
  9. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src/java_codebase_rag/analysis}/pr_analysis.py +1 -1
  10. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src/java_codebase_rag/analysis}/resolve_service.py +73 -6
  11. java_codebase_rag-0.9.6/src/java_codebase_rag/ast/__init__.py +0 -0
  12. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src/java_codebase_rag/ast}/ast_java.py +5 -5
  13. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src}/java_codebase_rag/cli.py +13 -18
  14. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src}/java_codebase_rag/config.py +116 -0
  15. java_codebase_rag-0.9.6/src/java_codebase_rag/graph/__init__.py +0 -0
  16. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src/java_codebase_rag/graph}/build_ast_graph.py +89 -11
  17. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src/java_codebase_rag/graph}/graph_enrich.py +248 -3
  18. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src/java_codebase_rag/graph}/graph_types.py +6 -2
  19. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src/java_codebase_rag/graph}/java_ontology.py +1 -1
  20. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src/java_codebase_rag/graph}/ladybug_queries.py +6 -6
  21. java_codebase_rag-0.9.6/src/java_codebase_rag/index/__init__.py +0 -0
  22. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src/java_codebase_rag/index}/java_index_flow_lancedb.py +30 -10
  23. java_codebase_rag-0.9.6/src/java_codebase_rag/install_data/__init__.py +0 -0
  24. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src}/java_codebase_rag/jrag.py +71 -16
  25. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src}/java_codebase_rag/jrag_envelope.py +13 -4
  26. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src}/java_codebase_rag/jrag_hints.py +1 -1
  27. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src}/java_codebase_rag/jrag_render.py +67 -3
  28. java_codebase_rag-0.9.6/src/java_codebase_rag/mcp/__init__.py +0 -0
  29. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src/java_codebase_rag/mcp}/mcp_hints.py +1 -1
  30. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src/java_codebase_rag/mcp}/mcp_v2.py +280 -81
  31. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src/java_codebase_rag/mcp}/server.py +138 -54
  32. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src}/java_codebase_rag/pipeline.py +26 -7
  33. java_codebase_rag-0.9.6/src/java_codebase_rag/search/__init__.py +0 -0
  34. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src/java_codebase_rag/search}/search_lancedb.py +53 -314
  35. java_codebase_rag-0.9.6/src/java_codebase_rag/search/search_lexical.py +329 -0
  36. java_codebase_rag-0.9.6/src/java_codebase_rag/search/search_scoring.py +338 -0
  37. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src/java_codebase_rag.egg-info}/PKG-INFO +2 -2
  38. java_codebase_rag-0.9.6/src/java_codebase_rag.egg-info/SOURCES.txt +60 -0
  39. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src}/java_codebase_rag.egg-info/entry_points.txt +1 -1
  40. java_codebase_rag-0.9.6/src/java_codebase_rag.egg-info/top_level.txt +1 -0
  41. java_codebase_rag-0.9.4/java_codebase_rag.egg-info/SOURCES.txt +0 -117
  42. java_codebase_rag-0.9.4/java_codebase_rag.egg-info/top_level.txt +0 -19
  43. java_codebase_rag-0.9.4/tests/test_agent_skills_static.py +0 -279
  44. java_codebase_rag-0.9.4/tests/test_assign_endpoint_client_extraction.py +0 -198
  45. java_codebase_rag-0.9.4/tests/test_ast_graph_build.py +0 -707
  46. java_codebase_rag-0.9.4/tests/test_ast_java_calls.py +0 -351
  47. java_codebase_rag-0.9.4/tests/test_ast_java_capabilities.py +0 -150
  48. java_codebase_rag-0.9.4/tests/test_ast_java_thread_safety.py +0 -66
  49. java_codebase_rag-0.9.4/tests/test_bank_chat_brownfield_integration.py +0 -95
  50. java_codebase_rag-0.9.4/tests/test_brownfield_clients.py +0 -374
  51. java_codebase_rag-0.9.4/tests/test_brownfield_events.py +0 -56
  52. java_codebase_rag-0.9.4/tests/test_brownfield_overrides.py +0 -587
  53. java_codebase_rag-0.9.4/tests/test_brownfield_routes.py +0 -344
  54. java_codebase_rag-0.9.4/tests/test_call_edge_matching.py +0 -121
  55. java_codebase_rag-0.9.4/tests/test_call_edges_e2e.py +0 -209
  56. java_codebase_rag-0.9.4/tests/test_call_graph_receiver_resolution.py +0 -159
  57. java_codebase_rag-0.9.4/tests/test_call_graph_smoke_roundtrip.py +0 -366
  58. java_codebase_rag-0.9.4/tests/test_call_invariant.py +0 -34
  59. java_codebase_rag-0.9.4/tests/test_cli_progress_stdout_invariant.py +0 -290
  60. java_codebase_rag-0.9.4/tests/test_cli_quiet_parity.py +0 -172
  61. java_codebase_rag-0.9.4/tests/test_client_hint_recovery.py +0 -126
  62. java_codebase_rag-0.9.4/tests/test_client_node_extraction.py +0 -254
  63. java_codebase_rag-0.9.4/tests/test_client_role_rename.py +0 -158
  64. java_codebase_rag-0.9.4/tests/test_config.py +0 -705
  65. java_codebase_rag-0.9.4/tests/test_cross_service_resolution_flag.py +0 -263
  66. java_codebase_rag-0.9.4/tests/test_edge_navigation_doc.py +0 -34
  67. java_codebase_rag-0.9.4/tests/test_fd_limit.py +0 -90
  68. java_codebase_rag-0.9.4/tests/test_feign_not_exposer.py +0 -164
  69. java_codebase_rag-0.9.4/tests/test_graph_enrich.py +0 -117
  70. java_codebase_rag-0.9.4/tests/test_graph_only_boot.py +0 -102
  71. java_codebase_rag-0.9.4/tests/test_incremental_graph.py +0 -1684
  72. java_codebase_rag-0.9.4/tests/test_install_data_sync.py +0 -249
  73. java_codebase_rag-0.9.4/tests/test_installer.py +0 -1784
  74. java_codebase_rag-0.9.4/tests/test_installer_integration.py +0 -135
  75. java_codebase_rag-0.9.4/tests/test_installer_surface.py +0 -911
  76. java_codebase_rag-0.9.4/tests/test_java_codebase_rag_cli.py +0 -1610
  77. java_codebase_rag-0.9.4/tests/test_jrag_auto_scope.py +0 -271
  78. java_codebase_rag-0.9.4/tests/test_jrag_enum_choices.py +0 -76
  79. java_codebase_rag-0.9.4/tests/test_jrag_envelope.py +0 -711
  80. java_codebase_rag-0.9.4/tests/test_jrag_listing.py +0 -458
  81. java_codebase_rag-0.9.4/tests/test_jrag_locate.py +0 -515
  82. java_codebase_rag-0.9.4/tests/test_jrag_orientation.py +0 -1129
  83. java_codebase_rag-0.9.4/tests/test_jrag_render.py +0 -854
  84. java_codebase_rag-0.9.4/tests/test_jrag_status.py +0 -218
  85. java_codebase_rag-0.9.4/tests/test_jrag_token_budget.py +0 -127
  86. java_codebase_rag-0.9.4/tests/test_jrag_traversal_compose.py +0 -727
  87. java_codebase_rag-0.9.4/tests/test_jrag_traversal_direct.py +0 -1000
  88. java_codebase_rag-0.9.4/tests/test_ladybug_queries.py +0 -576
  89. java_codebase_rag-0.9.4/tests/test_lance_optimize.py +0 -278
  90. java_codebase_rag-0.9.4/tests/test_lancedb_e2e.py +0 -388
  91. java_codebase_rag-0.9.4/tests/test_mcp_hints.py +0 -1322
  92. java_codebase_rag-0.9.4/tests/test_mcp_server_project_root.py +0 -126
  93. java_codebase_rag-0.9.4/tests/test_mcp_tools.py +0 -113
  94. java_codebase_rag-0.9.4/tests/test_mcp_v2.py +0 -2013
  95. java_codebase_rag-0.9.4/tests/test_mcp_v2_compose.py +0 -977
  96. java_codebase_rag-0.9.4/tests/test_meta_chain_core.py +0 -74
  97. java_codebase_rag-0.9.4/tests/test_microservice_scope.py +0 -270
  98. java_codebase_rag-0.9.4/tests/test_outgoing_call_extraction.py +0 -196
  99. java_codebase_rag-0.9.4/tests/test_packaging_metadata.py +0 -52
  100. java_codebase_rag-0.9.4/tests/test_path_filtering.py +0 -356
  101. java_codebase_rag-0.9.4/tests/test_pipeline.py +0 -103
  102. java_codebase_rag-0.9.4/tests/test_pr_analysis.py +0 -415
  103. java_codebase_rag-0.9.4/tests/test_progress.py +0 -463
  104. java_codebase_rag-0.9.4/tests/test_resolve_routes_messaging_layer_c.py +0 -102
  105. java_codebase_rag-0.9.4/tests/test_resolve_service.py +0 -220
  106. java_codebase_rag-0.9.4/tests/test_route_extraction.py +0 -415
  107. java_codebase_rag-0.9.4/tests/test_schema_consistency.py +0 -111
  108. java_codebase_rag-0.9.4/tests/test_search_lancedb.py +0 -558
  109. java_codebase_rag-0.9.4/tests/test_search_lancedb_capability.py +0 -127
  110. java_codebase_rag-0.9.4/tests/test_string_value_atoms.py +0 -23
  111. java_codebase_rag-0.9.4/tests/test_vectors_progress.py +0 -349
  112. java_codebase_rag-0.9.4/tests/test_version_flag.py +0 -39
  113. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6}/LICENSE +0 -0
  114. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6}/setup.cfg +0 -0
  115. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src}/java_codebase_rag/__init__.py +0 -0
  116. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src}/java_codebase_rag/_fdlimit.py +0 -0
  117. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src}/java_codebase_rag/_stdio.py +0 -0
  118. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src}/java_codebase_rag/_version.py +0 -0
  119. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src/java_codebase_rag/ast}/brownfield_events.py +0 -0
  120. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src/java_codebase_rag/ast}/chunk_heuristics.py +0 -0
  121. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src}/java_codebase_rag/cli_format.py +0 -0
  122. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src}/java_codebase_rag/cli_progress.py +0 -0
  123. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src/java_codebase_rag/graph}/path_filtering.py +0 -0
  124. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src/java_codebase_rag/index}/java_index_v1_common.py +0 -0
  125. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src}/java_codebase_rag/install_data/agents/explorer-rag-cli.md +0 -0
  126. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src}/java_codebase_rag/install_data/agents/explorer-rag-enhanced.md +0 -0
  127. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src}/java_codebase_rag/install_data/skills/explore-codebase/SKILL.md +0 -0
  128. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src}/java_codebase_rag/install_data/skills/explore-codebase-cli/SKILL.md +0 -0
  129. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src}/java_codebase_rag/installer.py +0 -0
  130. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src}/java_codebase_rag/lance_optimize.py +0 -0
  131. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src}/java_codebase_rag/progress.py +0 -0
  132. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src/java_codebase_rag/search}/index_common.py +0 -0
  133. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src}/java_codebase_rag.egg-info/dependency_links.txt +0 -0
  134. {java_codebase_rag-0.9.4 → java_codebase_rag-0.9.6/src}/java_codebase_rag.egg-info/requires.txt +0 -0
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: java-codebase-rag
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- Version: 0.9.4
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+ Version: 0.9.6
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  Summary: MCP server for semantic + structural search over Java codebases
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  Author: HumanBean17
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  License-Expression: MIT
@@ -86,7 +86,7 @@ The rest of this README is the install, the tool/command orientation, and the re
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  pip install java-codebase-rag
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  ```
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89
- Python **3.11+** required, on **Linux, macOS, and Windows**. On Linux, Windows, and **Apple Silicon** Macs every native dependency (LanceDB, LadybugDB/kuzu, CocoIndex) ships a wheel and you get the full semantic + graph search. **Intel Macs (x86_64) install graph-only**: PyTorch ≥2.3 and LanceDB ≥0.26 dropped macOS Intel wheels, so the vector stack is auto-excluded via PEP 508 markers — `pip install java-codebase-rag` works out of the box, the graph layer (`find` / `describe` / `neighbors` / `resolve`) is fully usable, and the `search` (semantic) tool reports it is unavailable rather than failing. After install, `java-codebase-rag --help` should print the CLI groups.
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+ Python **3.11+** required, on **Linux, macOS, and Windows**. On Linux, Windows, and **Apple Silicon** Macs every native dependency (LanceDB, LadybugDB/kuzu, CocoIndex) ships a wheel and you get the full semantic + graph search. **Intel Macs (x86_64) install graph-only**: PyTorch ≥2.3 and LanceDB ≥0.26 dropped macOS Intel wheels, so the vector stack is auto-excluded via PEP 508 markers — `pip install java-codebase-rag` works out of the box, the graph layer (`find` / `describe` / `neighbors` / `resolve`) is fully usable, and the `search` tool falls back to **lexical (keyword) search** over the symbol graph (same tool contract, keyword-ranked instead of semantic; an advisory notes the mode). Semantic/vector search needs Apple Silicon, Linux, or Windows. After install, `java-codebase-rag --help` should print the CLI groups.
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  The package includes the CocoIndex lifecycle dependency used by `init`, `increment`, `reprocess`, and `erase` on platforms that have it (it is absent on Intel Mac).
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  ### Interactive setup (recommended)
@@ -41,7 +41,7 @@ The rest of this README is the install, the tool/command orientation, and the re
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  pip install java-codebase-rag
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42
  ```
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43
 
44
- Python **3.11+** required, on **Linux, macOS, and Windows**. On Linux, Windows, and **Apple Silicon** Macs every native dependency (LanceDB, LadybugDB/kuzu, CocoIndex) ships a wheel and you get the full semantic + graph search. **Intel Macs (x86_64) install graph-only**: PyTorch ≥2.3 and LanceDB ≥0.26 dropped macOS Intel wheels, so the vector stack is auto-excluded via PEP 508 markers — `pip install java-codebase-rag` works out of the box, the graph layer (`find` / `describe` / `neighbors` / `resolve`) is fully usable, and the `search` (semantic) tool reports it is unavailable rather than failing. After install, `java-codebase-rag --help` should print the CLI groups.
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+ Python **3.11+** required, on **Linux, macOS, and Windows**. On Linux, Windows, and **Apple Silicon** Macs every native dependency (LanceDB, LadybugDB/kuzu, CocoIndex) ships a wheel and you get the full semantic + graph search. **Intel Macs (x86_64) install graph-only**: PyTorch ≥2.3 and LanceDB ≥0.26 dropped macOS Intel wheels, so the vector stack is auto-excluded via PEP 508 markers — `pip install java-codebase-rag` works out of the box, the graph layer (`find` / `describe` / `neighbors` / `resolve`) is fully usable, and the `search` tool falls back to **lexical (keyword) search** over the symbol graph (same tool contract, keyword-ranked instead of semantic; an advisory notes the mode). Semantic/vector search needs Apple Silicon, Linux, or Windows. After install, `java-codebase-rag --help` should print the CLI groups.
45
45
  The package includes the CocoIndex lifecycle dependency used by `init`, `increment`, `reprocess`, and `erase` on platforms that have it (it is absent on Intel Mac).
46
46
 
47
47
  ### Interactive setup (recommended)
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
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5
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  [project]
6
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  name = "java-codebase-rag"
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- version = "0.9.4"
7
+ version = "0.9.6"
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  description = "MCP server for semantic + structural search over Java codebases"
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  readme = "README.md"
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  requires-python = ">=3.11"
@@ -28,7 +28,9 @@ classifiers = [
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  # The vector/semantic-search trio (cocoindex[lancedb], lancedb, sentence-transformers
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  # -> torch) is gated off on Intel Mac (darwin + x86_64): torch >=2.3 and lancedb >=0.26
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  # dropped macOS x86_64 wheels, so the full stack is uninstallable there. On Intel Mac the
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- # package installs graph-only and works out of the box; every other platform is unchanged.
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+ # package installs graph-only and works out of the box `search` then falls back to the
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+ # lexical (keyword) backend over the symbol graph (search_lexical.py); every other platform
33
+ # is unchanged.
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  dependencies = [
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  "cocoindex[lancedb]>=1.0.7,<2; sys_platform != 'darwin' or platform_machine != 'x86_64'",
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  "ladybug>=0.17.1,<0.18",
@@ -62,31 +64,11 @@ Issues = "https://github.com/HumanBean17/java-codebase-rag/issues"
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63
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  [project.scripts]
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  java-codebase-rag = "java_codebase_rag.cli:_console_script_main"
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- java-codebase-rag-mcp = "server:main"
67
+ java-codebase-rag-mcp = "java_codebase_rag.mcp.server:main"
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68
  jrag = "java_codebase_rag.jrag:_console_script_main"
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68
- [tool.setuptools]
69
- packages = ["java_codebase_rag"]
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- py-modules = [
71
- "ast_java",
72
- "brownfield_events",
73
- "build_ast_graph",
74
- "chunk_heuristics",
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- "graph_enrich",
76
- "graph_types",
77
- "index_common",
78
- "java_index_flow_lancedb",
79
- "java_index_v1_common",
80
- "java_ontology",
81
- "ladybug_queries",
82
- "mcp_hints",
83
- "mcp_v2",
84
- "path_filtering",
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- "pr_analysis",
86
- "resolve_service",
87
- "search_lancedb",
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- "server",
89
- ]
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+ [tool.setuptools.packages.find]
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+ where = ["src"]
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91
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  [tool.ruff]
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  line-length = 100