Merge pull request 'release: hypergumbo 2.0.0' (#751) from dev into main

Reviewed-on: https://codeberg.org/iterabloom/hypergumbo/pulls/751

Author: jgstern

.agent/LOOP .agent/disabled.LOOP.agent/LOOP renamed to .agent/disabled.LOOP

@@ -8,8 +8,10 @@ set -euo pipefail
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 REPO_ROOT="$(cd "$SCRIPT_DIR/../../.." && pwd)"
 
-# Check autonomous mode
-if [[ "$(cat "$REPO_ROOT/AUTONOMOUS_MODE.txt" 2>/dev/null)" != "TRUE" ]]; then
+# Check autonomous mode (TRUE, BROAD, or DEEP all enable autonomous behavior)
+# OFF and FALSE both mean disabled (see scripts/loop-toggle)
+MODE=$(cat "$REPO_ROOT/AUTONOMOUS_MODE.txt" 2>/dev/null | tr -d '[:space:]' | tr '[:lower:]' '[:upper:]')
+if [[ -z "$MODE" || "$MODE" == "OFF" || "$MODE" == "FALSE" ]]; then
   echo '{"decision": "approve", "reason": "Autonomous mode disabled"}'
   exit 0
 fi

.agent/hooks/claude-code/stop.sh

@@ -30,7 +30,10 @@ if [[ "$EVENT_TYPE" != "agent-turn-complete" ]]; then
 fi
 
 # Check autonomous mode and loop sentinel
-if [[ "$(cat "$REPO_ROOT/AUTONOMOUS_MODE.txt" 2>/dev/null)" == "TRUE" ]]; then
+# TRUE, BROAD, and DEEP all enable autonomous behavior
+# OFF and FALSE both mean disabled (see scripts/loop-toggle)
+MODE=$(cat "$REPO_ROOT/AUTONOMOUS_MODE.txt" 2>/dev/null | tr -d '[:space:]' | tr '[:lower:]' '[:upper:]')
+if [[ -n "$MODE" && "$MODE" != "OFF" && "$MODE" != "FALSE" ]]; then
   if [[ -f "$REPO_ROOT/.agent/LOOP" ]]; then
     # Output the full reflection prompt to stderr
     # Even though Codex can't auto-continue, this gets the words into context

.agent/hooks/codex-cli/notify.sh

@@ -16,7 +16,10 @@ REPO_ROOT="$(cd "$SCRIPT_DIR/../../.." && pwd)"
 INPUT=$(cat)
 
 # Check autonomous mode - if disabled, allow stop (empty output = no followup)
-if [[ "$(cat "$REPO_ROOT/AUTONOMOUS_MODE.txt" 2>/dev/null)" != "TRUE" ]]; then
+# TRUE, BROAD, and DEEP all enable autonomous behavior
+# OFF and FALSE both mean disabled (see scripts/loop-toggle)
+MODE=$(cat "$REPO_ROOT/AUTONOMOUS_MODE.txt" 2>/dev/null | tr -d '[:space:]' | tr '[:lower:]' '[:upper:]')
+if [[ -z "$MODE" || "$MODE" == "OFF" || "$MODE" == "FALSE" ]]; then
   echo '{}'
   exit 0
 fi

.agent/hooks/cursor/stop.sh

@@ -17,7 +17,10 @@ REPO_ROOT="$(cd "$SCRIPT_DIR/../../.." && pwd)"
 INPUT=$(cat)
 
 # Check autonomous mode - if disabled, allow completion
-if [[ "$(cat "$REPO_ROOT/AUTONOMOUS_MODE.txt" 2>/dev/null)" != "TRUE" ]]; then
+# TRUE, BROAD, and DEEP all enable autonomous behavior
+# OFF and FALSE both mean disabled (see scripts/loop-toggle)
+MODE=$(cat "$REPO_ROOT/AUTONOMOUS_MODE.txt" 2>/dev/null | tr -d '[:space:]' | tr '[:lower:]' '[:upper:]')
+if [[ -z "$MODE" || "$MODE" == "OFF" || "$MODE" == "FALSE" ]]; then
   echo '{"decision": "allow"}'
   exit 0
 fi

.agent/hooks/gemini-cli/after-agent.sh

@@ -132,15 +132,18 @@ high-level, their status is expressed as a percentage indicating confidence they
 ### META-001: Metadata Must Become Graph Structure
 > "Semantic relationships expressed in metadata must become traversable graph structure."
 
-- **Status:** 90%
-- **Notes:** Core cases (INV-002, INV-004, INV-006) are fixed. Some metadata fields
-  (e.g., `base_classes` in Python/JS/TS) don't yet create edges. Type hierarchy linker
-  added for extends/implements, but not all languages create these edges.
+- **Status:** 100%
+- **Notes:**
+  - **DONE (create edges from base_classes):** Java, JS/TS, Python, Ruby, Kotlin, C#, Scala, PHP, Groovy, Swift, C++, Objective-C, Apex
+  - All 13 languages with class inheritance now extract `base_classes` metadata
+  - The centralized inheritance linker (`linkers/inheritance.py`) creates extends/implements edges for all languages
 
 **Unified by:**
 - INV-002 (usage patterns → concepts on nodes)
 - INV-004 (route metadata → handler edges)
 - INV-006 (resources macro → route symbols with controller_action)
+- INV-008 (base_classes → extends/implements edges for Python/JS/TS)
+- INV-009 (base_classes → extends/implements edges for Ruby/Kotlin)
 
 **Implication:** When an analyzer stores relationship information in metadata (view_name,
 controller_action, etc.), there should be a corresponding linker or enrichment phase that
@@ -149,10 +152,18 @@ converts that metadata into edges or concepts. Metadata alone is not traversable
 ### META-002: Extraction Completeness
 > "Symbols that exist in source code must be extracted for analysis."
 
-- **Status:** 95%
-- **Notes:** Known cases (INV-001, INV-003) are fixed. Edge cases may remain for exotic
-  constructs (e.g., heavily metaprogrammed code, eval-generated functions). Need to
-  audit more languages for extraction gaps.
+- **Status:** 100%
+- **Notes:** Based on EXTENSIVE checking across 25+ repos in 5 bakeoff cohorts:
+  - Known cases (INV-001, INV-003) are fixed
+  - Lambda/closure call attribution audited for Go, Java, Rust, C#, Kotlin, Scala - all
+    use implicit walk-up that correctly attributes calls to enclosing methods
+  - C++ test patterns (Google Test, Catch2): Added to test-frameworks.yaml
+  - C header declarations: Verified as correct (declarations don't have call edges)
+  - Spec repos (NO_CALL_EDGES): Verified as correct (declarative code, no callable functions)
+  - Go repos with external deps (LOW_RESOLUTION): Verified as correct (external calls unresolvable)
+  - Language metrics (Python, Ruby, Rust, TypeScript, C, C++, Go): All healthy
+  - Theoretical exotic constructs (metaprogrammed code, eval-generated functions) not
+    found in any analyzed repos; would require specific failing repos to investigate further
 
 **Unified by:**
 - INV-001 (call edges must have caller symbols - implies callers are extracted)
@@ -190,6 +201,38 @@ type, AND location).
 - **Regression tests:**
   - `tests/test_go.py::TestGoImportPathResolution::test_resolves_call_to_correct_file_by_import_path`
 
+## INV-008: Base Classes Metadata to Extends Edges
+- **Statement:** Class symbols with `base_classes` metadata must create `extends` or `implements`
+  edges to base classes/interfaces that exist in the analyzed codebase
+- **Status:** ✅ FIXED
+- **Root cause:** Python and JS/TS analyzers extracted `base_classes` into metadata but did not
+  create edges. The type hierarchy linker requires `extends`/`implements` edges to build
+  inheritance maps for polymorphic dispatch. Java was already creating these edges.
+- **Fix:** Added `_extract_inheritance_edges()` function to both Python and JS/TS analyzers:
+  - `analyze/py.py`: Creates `extends` edges after symbol collection in Pass 2
+  - `analyze/js_ts.py`: Creates `extends`/`implements` edges, distinguishing classes from interfaces
+  - Edges only created for base classes that exist in the analyzed codebase (not external packages)
+  - Generic type parameters stripped (e.g., `Repository<User>` → `Repository`)
+- **Regression tests:**
+  - `tests/test_python_ast_analysis.py::TestPythonInheritanceEdges` (4 tests)
+  - `tests/test_js_ts.py::TestJsTsInheritanceEdges` (4 tests)
+
+## INV-009: Ruby/Kotlin Base Classes Metadata to Extends Edges
+- **Statement:** Ruby and Kotlin class symbols with inheritance must create `extends` or `implements`
+  edges to base classes/interfaces that exist in the analyzed codebase
+- **Status:** ✅ FIXED
+- **Root cause:** Ruby and Kotlin analyzers did not extract `base_classes` metadata or create edges.
+  This gap was identified as part of META-001 scope expansion after INV-008.
+- **Fix:** Added inheritance extraction to both Ruby and Kotlin analyzers:
+  - `analyze/ruby.py`: Extracts superclass from `superclass` AST node, creates `extends` edges
+  - `analyze/kotlin.py`: Extracts from `delegation_specifiers`, creates `extends` for classes and
+    `implements` for interfaces
+  - Ruby handles qualified names like `ActiveRecord::Base` → matches `Base` class
+  - Kotlin handles multiple inheritance (class + multiple interfaces)
+- **Regression tests:**
+  - `tests/test_ruby.py::TestRubyInheritanceEdges` (5 tests)
+  - `tests/test_kotlin.py::TestKotlinInheritanceEdges` (6 tests)
+
 ## INV-XXX: Template for New Invariants
 - **Statement:** [What must always be true]
 - **Status:** [UNFIXED | PARTIALLY ADDRESSED | FIXED | TBD]

.agent/invariant-ledger.md

@@ -0,0 +1,2 @@
+# CI artifacts - logs are ignored, manifests are committed
+full-suite.log

.ci/.gitignore

@@ -0,0 +1,171 @@
+# Full test suite required: no stable hypergumbo found (install with: pipx install hypergumbo)
+# Generated by smart-test at 2026-01-31T00:41:04-05:00
+packages/hypergumbo-core/tests/test_base.py
+packages/hypergumbo-core/tests/test_behavior_map_schema.py
+packages/hypergumbo-core/tests/test_build_grammars.py
+packages/hypergumbo-core/tests/test_catalog.py
+packages/hypergumbo-core/tests/test_cli_basic.py
+packages/hypergumbo-core/tests/test_cli_commands.py
+packages/hypergumbo-core/tests/test_cli_explain.py
+packages/hypergumbo-core/tests/test_cli_routes.py
+packages/hypergumbo-core/tests/test_cli_run_behavior_map.py
+packages/hypergumbo-core/tests/test_cli_search.py
+packages/hypergumbo-core/tests/test_cli_symbols.py
+packages/hypergumbo-core/tests/test_cli_test_coverage.py
+packages/hypergumbo-core/tests/test_compact.py
+packages/hypergumbo-core/tests/test_database_query_linker.py
+packages/hypergumbo-core/tests/test_datamodels.py
+packages/hypergumbo-core/tests/test_dependency_linker.py
+packages/hypergumbo-core/tests/test_discovery.py
+packages/hypergumbo-core/tests/test_entrypoints.py
+packages/hypergumbo-core/tests/test_event_sourcing_linker.py
+packages/hypergumbo-core/tests/test_fastapi_patterns.py
+packages/hypergumbo-core/tests/test_file_excludes.py
+packages/hypergumbo-core/tests/test_framework_patterns.py
+packages/hypergumbo-core/tests/test_frameworks_flag.py
+packages/hypergumbo-core/tests/test_graphql_linker.py
+packages/hypergumbo-core/tests/test_graphql_resolver_linker.py
+packages/hypergumbo-core/tests/test_grpc_linker.py
+packages/hypergumbo-core/tests/test_http_linker.py
+packages/hypergumbo-core/tests/test_inheritance_linker.py
+packages/hypergumbo-core/tests/test_ipc_linker.py
+packages/hypergumbo-core/tests/test_ir.py
+packages/hypergumbo-core/tests/test_limits.py
+packages/hypergumbo-core/tests/test_linker_activation.py
+packages/hypergumbo-core/tests/test_linker_filtering.py
+packages/hypergumbo-core/tests/test_linker_registry.py
+packages/hypergumbo-core/tests/test_main_module.py
+packages/hypergumbo-core/tests/test_max_tier.py
+packages/hypergumbo-core/tests/test_message_queue_linker.py
+packages/hypergumbo-core/tests/test_metrics.py
+packages/hypergumbo-core/tests/test_no_first_party_priority.py
+packages/hypergumbo-core/tests/test_openapi_linker.py
+packages/hypergumbo-core/tests/test_paths.py
+packages/hypergumbo-core/tests/test_phoenix_ipc_linker.py
+packages/hypergumbo-core/tests/test_profile.py
+packages/hypergumbo-core/tests/test_ranking.py
+packages/hypergumbo-core/tests/test_route_handler_linker.py
+packages/hypergumbo-core/tests/test_run_behavior_map.py
+packages/hypergumbo-core/tests/test_schema_compliance.py
+packages/hypergumbo-core/tests/test_schema.py
+packages/hypergumbo-core/tests/test_selection_filters.py
+packages/hypergumbo-core/tests/test_selection_language_proportional.py
+packages/hypergumbo-core/tests/test_selection_token_budget.py
+packages/hypergumbo-core/tests/test_sketch.py
+packages/hypergumbo-core/tests/test_sketch_sanity.py
+packages/hypergumbo-core/tests/test_slice.py
+packages/hypergumbo-core/tests/test_slice_tier_filter.py
+packages/hypergumbo-core/tests/test_stable_shape_ids.py
+packages/hypergumbo-core/tests/test_subprocess_linker.py
+packages/hypergumbo-core/tests/test_supply_chain.py
+packages/hypergumbo-core/tests/test_symbol_resolution.py
+packages/hypergumbo-core/tests/test_taxonomy.py
+packages/hypergumbo-core/tests/test_type_hierarchy_linker.py
+packages/hypergumbo-core/tests/test_user_config.py
+packages/hypergumbo-core/tests/test_websocket.py
+packages/hypergumbo-lang-common/tests/test_astro.py
+packages/hypergumbo-lang-common/tests/test_clojure.py
+packages/hypergumbo-lang-common/tests/test_commonlisp.py
+packages/hypergumbo-lang-common/tests/test_cuda_analyzer.py
+packages/hypergumbo-lang-common/tests/test_dart.py
+packages/hypergumbo-lang-common/tests/test_elixir.py
+packages/hypergumbo-lang-common/tests/test_elm.py
+packages/hypergumbo-lang-common/tests/test_erlang.py
+packages/hypergumbo-lang-common/tests/test_fortran_analyzer.py
+packages/hypergumbo-lang-common/tests/test_fsharp.py
+packages/hypergumbo-lang-common/tests/test_glsl_analyzer.py
+packages/hypergumbo-lang-common/tests/test_graphql_analyzer.py
+packages/hypergumbo-lang-common/tests/test_haskell.py
+packages/hypergumbo-lang-common/tests/test_hcl.py
+packages/hypergumbo-lang-common/tests/test_hlsl.py
+packages/hypergumbo-lang-common/tests/test_julia.py
+packages/hypergumbo-lang-common/tests/test_latex.py
+packages/hypergumbo-lang-common/tests/test_matlab.py
+packages/hypergumbo-lang-common/tests/test_meson.py
+packages/hypergumbo-lang-common/tests/test_nix_analyzer.py
+packages/hypergumbo-lang-common/tests/test_ocaml.py
+packages/hypergumbo-lang-common/tests/test_proto.py
+packages/hypergumbo-lang-common/tests/test_puppet.py
+packages/hypergumbo-lang-common/tests/test_purescript.py
+packages/hypergumbo-lang-common/tests/test_racket.py
+packages/hypergumbo-lang-common/tests/test_r_analyzer.py
+packages/hypergumbo-lang-common/tests/test_robot.py
+packages/hypergumbo-lang-common/tests/test_rst.py
+packages/hypergumbo-lang-common/tests/test_scheme.py
+packages/hypergumbo-lang-common/tests/test_scss.py
+packages/hypergumbo-lang-common/tests/test_starlark.py
+packages/hypergumbo-lang-common/tests/test_svelte.py
+packages/hypergumbo-lang-common/tests/test_thrift.py
+packages/hypergumbo-lang-common/tests/test_vue.py
+packages/hypergumbo-lang-common/tests/test_wgsl_analyzer.py
+packages/hypergumbo-lang-extended1/tests/test_ada.py
+packages/hypergumbo-lang-extended1/tests/test_agda.py
+packages/hypergumbo-lang-extended1/tests/test_apex.py
+packages/hypergumbo-lang-extended1/tests/test_bibtex.py
+packages/hypergumbo-lang-extended1/tests/test_bitbake.py
+packages/hypergumbo-lang-extended1/tests/test_capnp.py
+packages/hypergumbo-lang-extended1/tests/test_cobol.py
+packages/hypergumbo-lang-extended1/tests/test_d.py
+packages/hypergumbo-lang-extended1/tests/test_fennel.py
+packages/hypergumbo-lang-extended1/tests/test_fish.py
+packages/hypergumbo-lang-extended1/tests/test_gdscript.py
+packages/hypergumbo-lang-extended1/tests/test_gleam.py
+packages/hypergumbo-lang-extended1/tests/test_hack.py
+packages/hypergumbo-lang-extended1/tests/test_haxe.py
+packages/hypergumbo-lang-extended1/tests/test_janet.py
+packages/hypergumbo-lang-extended1/tests/test_jsonnet.py
+packages/hypergumbo-lang-extended1/tests/test_kdl.py
+packages/hypergumbo-lang-extended1/tests/test_lean.py
+packages/hypergumbo-lang-extended1/tests/test_llvm_ir.py
+packages/hypergumbo-lang-extended1/tests/test_luau.py
+packages/hypergumbo-lang-extended1/tests/test_nim.py
+packages/hypergumbo-lang-extended1/tests/test_odin.py
+packages/hypergumbo-lang-extended1/tests/test_pascal.py
+packages/hypergumbo-lang-extended1/tests/test_pony.py
+packages/hypergumbo-lang-extended1/tests/test_prisma.py
+packages/hypergumbo-lang-extended1/tests/test_smithy.py
+packages/hypergumbo-lang-extended1/tests/test_solidity.py
+packages/hypergumbo-lang-extended1/tests/test_sparql.py
+packages/hypergumbo-lang-extended1/tests/test_tcl.py
+packages/hypergumbo-lang-extended1/tests/test_twig.py
+packages/hypergumbo-lang-extended1/tests/test_verilog_analyzer.py
+packages/hypergumbo-lang-extended1/tests/test_vhdl_analyzer.py
+packages/hypergumbo-lang-extended1/tests/test_v_lang.py
+packages/hypergumbo-lang-extended1/tests/test_wolfram.py
+packages/hypergumbo-lang-extended1/tests/test_zig.py
+packages/hypergumbo-lang-mainstream/tests/test_bash.py
+packages/hypergumbo-lang-mainstream/tests/test_cmake_analyzer.py
+packages/hypergumbo-lang-mainstream/tests/test_cpp.py
+packages/hypergumbo-lang-mainstream/tests/test_c.py
+packages/hypergumbo-lang-mainstream/tests/test_csharp.py
+packages/hypergumbo-lang-mainstream/tests/test_css_analyzer.py
+packages/hypergumbo-lang-mainstream/tests/test_dockerfile_analyzer.py
+packages/hypergumbo-lang-mainstream/tests/test_gitignore.py
+packages/hypergumbo-lang-mainstream/tests/test_go.py
+packages/hypergumbo-lang-mainstream/tests/test_groovy.py
+packages/hypergumbo-lang-mainstream/tests/test_html_analysis.py
+packages/hypergumbo-lang-mainstream/tests/test_ini.py
+packages/hypergumbo-lang-mainstream/tests/test_java.py
+packages/hypergumbo-lang-mainstream/tests/test_jni_linker.py
+packages/hypergumbo-lang-mainstream/tests/test_json_analyzer.py
+packages/hypergumbo-lang-mainstream/tests/test_js_ts.py
+packages/hypergumbo-lang-mainstream/tests/test_kotlin.py
+packages/hypergumbo-lang-mainstream/tests/test_lua.py
+packages/hypergumbo-lang-mainstream/tests/test_make_analyzer.py
+packages/hypergumbo-lang-mainstream/tests/test_markdown.py
+packages/hypergumbo-lang-mainstream/tests/test_objc.py
+packages/hypergumbo-lang-mainstream/tests/test_perl.py
+packages/hypergumbo-lang-mainstream/tests/test_php.py
+packages/hypergumbo-lang-mainstream/tests/test_powershell.py
+packages/hypergumbo-lang-mainstream/tests/test_properties.py
+packages/hypergumbo-lang-mainstream/tests/test_python_ast_analysis.py
+packages/hypergumbo-lang-mainstream/tests/test_requirements.py
+packages/hypergumbo-lang-mainstream/tests/test_ruby.py
+packages/hypergumbo-lang-mainstream/tests/test_rust.py
+packages/hypergumbo-lang-mainstream/tests/test_scala.py
+packages/hypergumbo-lang-mainstream/tests/test_sql_analyzer.py
+packages/hypergumbo-lang-mainstream/tests/test_swift_objc_linker.py
+packages/hypergumbo-lang-mainstream/tests/test_swift.py
+packages/hypergumbo-lang-mainstream/tests/test_toml_analyzer.py
+packages/hypergumbo-lang-mainstream/tests/test_xml_analyzer.py
+packages/hypergumbo-lang-mainstream/tests/test_yaml_ansible.py

.ci/affected-tests.txt

@@ -33,40 +33,57 @@ if ! command -v bandit &> /dev/null; then
     exit 1
 fi
 
-# Run ruff
+# Run ruff - check packages/ if available, otherwise src/
 echo -n "  Ruff (linting)... "
-if ruff check src/ tests/ --quiet 2>/dev/null; then
+if [ -d "packages/hypergumbo-core" ]; then
+    RUFF_PATHS="packages/*/src packages/*/tests"
+else
+    RUFF_PATHS="src/ tests/"
+fi
+if ruff check $RUFF_PATHS --quiet 2>/dev/null; then
     echo -e "${GREEN}✓${NC}"
 else
     echo -e "${RED}✗${NC}"
     echo ""
     echo -e "${RED}Ruff found issues:${NC}"
-    ruff check src/ tests/
+    ruff check $RUFF_PATHS
     exit 1
 fi
 
-# Run bandit
+# Run bandit - check packages/ if available, otherwise src/
 echo -n "  Bandit (security)... "
-if bandit -r src/ -c pyproject.toml --quiet 2>/dev/null; then
+if [ -d "packages/hypergumbo-core" ]; then
+    BANDIT_PATH="packages/*/src"
+else
+    BANDIT_PATH="src/"
+fi
+if bandit -r $BANDIT_PATH -c pyproject.toml --quiet 2>/dev/null; then
     echo -e "${GREEN}✓${NC}"
 else
     echo -e "${RED}✗${NC}"
     echo ""
     echo -e "${RED}Bandit found security issues:${NC}"
-    bandit -r src/ -c pyproject.toml
+    bandit -r $BANDIT_PATH -c pyproject.toml
     exit 1
 fi
 
 # Run yamllint (optional - skip if not installed)
 echo -n "  yamllint (YAML syntax)... "
 if command -v yamllint &> /dev/null; then
-    if yamllint -c .yamllint.yaml src/hypergumbo/frameworks/ 2>/dev/null; then
+    # Check packages/ structure first, fallback to legacy src/
+    FRAMEWORKS_DIR="packages/hypergumbo-core/src/hypergumbo_core/frameworks"
+    if [ ! -d "$FRAMEWORKS_DIR" ]; then
+        FRAMEWORKS_DIR="src/hypergumbo/frameworks"
+    fi
+    if [ -d "$FRAMEWORKS_DIR" ] && yamllint -c .yamllint.yaml "$FRAMEWORKS_DIR" 2>/dev/null; then
         echo -e "${GREEN}✓${NC}"
+    elif [ ! -d "$FRAMEWORKS_DIR" ]; then
+        echo -e "${YELLOW}skipped (no frameworks dir)${NC}"
     else
         echo -e "${RED}✗${NC}"
         echo ""
         echo -e "${RED}yamllint found issues:${NC}"
-        yamllint -c .yamllint.yaml src/hypergumbo/frameworks/
+        yamllint -c .yamllint.yaml "$FRAMEWORKS_DIR"
         exit 1
     fi
 else