npm - @optave/codegraph - Versions diffs - 3.9.6 → 3.11.0 - Mend

@optave/codegraph 3.9.6 → 3.11.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (186) hide show

package/README.md +26 -12
package/dist/ast-analysis/engine.d.ts.map +1 -1
package/dist/ast-analysis/engine.js +1 -1
package/dist/ast-analysis/engine.js.map +1 -1
package/dist/ast-analysis/rules/index.d.ts.map +1 -1
package/dist/ast-analysis/rules/index.js +77 -0
package/dist/ast-analysis/rules/index.js.map +1 -1
package/dist/ast-analysis/visitors/ast-store-visitor.d.ts.map +1 -1
package/dist/ast-analysis/visitors/ast-store-visitor.js +50 -8
package/dist/ast-analysis/visitors/ast-store-visitor.js.map +1 -1
package/dist/cli/commands/audit.js +1 -1
package/dist/cli/commands/audit.js.map +1 -1
package/dist/cli/commands/build.d.ts.map +1 -1
package/dist/cli/commands/build.js +2 -0
package/dist/cli/commands/build.js.map +1 -1
package/dist/cli/commands/check.js +1 -1
package/dist/cli/commands/check.js.map +1 -1
package/dist/cli/commands/children.js +1 -1
package/dist/cli/commands/children.js.map +1 -1
package/dist/cli/commands/diff-impact.js +1 -1
package/dist/cli/commands/diff-impact.js.map +1 -1
package/dist/cli/commands/roles.js +1 -1
package/dist/cli/commands/roles.js.map +1 -1
package/dist/cli/commands/structure.js +1 -1
package/dist/cli/commands/structure.js.map +1 -1
package/dist/cli/shared/options.js +1 -1
package/dist/cli/shared/options.js.map +1 -1
package/dist/db/connection.d.ts.map +1 -1
package/dist/db/connection.js +8 -0
package/dist/db/connection.js.map +1 -1
package/dist/domain/graph/builder/context.d.ts +10 -0
package/dist/domain/graph/builder/context.d.ts.map +1 -1
package/dist/domain/graph/builder/context.js +10 -0
package/dist/domain/graph/builder/context.js.map +1 -1
package/dist/domain/graph/builder/helpers.d.ts +7 -2
package/dist/domain/graph/builder/helpers.d.ts.map +1 -1
package/dist/domain/graph/builder/helpers.js +7 -2
package/dist/domain/graph/builder/helpers.js.map +1 -1
package/dist/domain/graph/builder/incremental.d.ts +0 -6
package/dist/domain/graph/builder/incremental.d.ts.map +1 -1
package/dist/domain/graph/builder/incremental.js +6 -23
package/dist/domain/graph/builder/incremental.js.map +1 -1
package/dist/domain/graph/builder/pipeline.d.ts +44 -0
package/dist/domain/graph/builder/pipeline.d.ts.map +1 -1
package/dist/domain/graph/builder/pipeline.js +348 -42
package/dist/domain/graph/builder/pipeline.js.map +1 -1
package/dist/domain/graph/builder/stages/build-edges.d.ts.map +1 -1
package/dist/domain/graph/builder/stages/build-edges.js +8 -2
package/dist/domain/graph/builder/stages/build-edges.js.map +1 -1
package/dist/domain/graph/builder/stages/collect-files.d.ts.map +1 -1
package/dist/domain/graph/builder/stages/collect-files.js +8 -0
package/dist/domain/graph/builder/stages/collect-files.js.map +1 -1
package/dist/domain/graph/builder/stages/detect-changes.d.ts +24 -0
package/dist/domain/graph/builder/stages/detect-changes.d.ts.map +1 -1
package/dist/domain/graph/builder/stages/detect-changes.js +117 -3
package/dist/domain/graph/builder/stages/detect-changes.js.map +1 -1
package/dist/domain/graph/builder/stages/finalize.d.ts.map +1 -1
package/dist/domain/graph/builder/stages/finalize.js +9 -6
package/dist/domain/graph/builder/stages/finalize.js.map +1 -1
package/dist/domain/graph/builder/stages/insert-nodes.d.ts +30 -0
package/dist/domain/graph/builder/stages/insert-nodes.d.ts.map +1 -1
package/dist/domain/graph/builder/stages/insert-nodes.js +36 -13
package/dist/domain/graph/builder/stages/insert-nodes.js.map +1 -1
package/dist/domain/graph/builder/stages/resolve-imports.d.ts.map +1 -1
package/dist/domain/graph/builder/stages/resolve-imports.js +73 -22
package/dist/domain/graph/builder/stages/resolve-imports.js.map +1 -1
package/dist/domain/graph/watcher.d.ts.map +1 -1
package/dist/domain/graph/watcher.js +23 -18
package/dist/domain/graph/watcher.js.map +1 -1
package/dist/domain/parser.d.ts +14 -1
package/dist/domain/parser.d.ts.map +1 -1
package/dist/domain/parser.js +104 -11
package/dist/domain/parser.js.map +1 -1
package/dist/domain/search/models.d.ts +16 -0
package/dist/domain/search/models.d.ts.map +1 -1
package/dist/domain/search/models.js +36 -2
package/dist/domain/search/models.js.map +1 -1
package/dist/domain/wasm-worker-entry.js +20 -13
package/dist/domain/wasm-worker-entry.js.map +1 -1
package/dist/extractors/c.js +25 -6
package/dist/extractors/c.js.map +1 -1
package/dist/extractors/cpp.js +47 -6
package/dist/extractors/cpp.js.map +1 -1
package/dist/extractors/cuda.js +90 -14
package/dist/extractors/cuda.js.map +1 -1
package/dist/extractors/elixir.js +83 -3
package/dist/extractors/elixir.js.map +1 -1
package/dist/extractors/erlang.js +56 -20
package/dist/extractors/erlang.js.map +1 -1
package/dist/extractors/fsharp.d.ts +7 -0
package/dist/extractors/fsharp.d.ts.map +1 -1
package/dist/extractors/fsharp.js +94 -0
package/dist/extractors/fsharp.js.map +1 -1
package/dist/extractors/gleam.js +6 -2
package/dist/extractors/gleam.js.map +1 -1
package/dist/extractors/groovy.js +41 -1
package/dist/extractors/groovy.js.map +1 -1
package/dist/extractors/haskell.js +48 -4
package/dist/extractors/haskell.js.map +1 -1
package/dist/extractors/julia.js +172 -41
package/dist/extractors/julia.js.map +1 -1
package/dist/extractors/kotlin.js +4 -0
package/dist/extractors/kotlin.js.map +1 -1
package/dist/extractors/objc.js +184 -47
package/dist/extractors/objc.js.map +1 -1
package/dist/extractors/python.js +7 -4
package/dist/extractors/python.js.map +1 -1
package/dist/extractors/r.js +93 -52
package/dist/extractors/r.js.map +1 -1
package/dist/extractors/scala.d.ts.map +1 -1
package/dist/extractors/scala.js +18 -32
package/dist/extractors/scala.js.map +1 -1
package/dist/extractors/solidity.js +18 -9
package/dist/extractors/solidity.js.map +1 -1
package/dist/extractors/verilog.js +80 -15
package/dist/extractors/verilog.js.map +1 -1
package/dist/infrastructure/config.d.ts +1 -0
package/dist/infrastructure/config.d.ts.map +1 -1
package/dist/infrastructure/config.js +1 -0
package/dist/infrastructure/config.js.map +1 -1
package/dist/mcp/server.d.ts.map +1 -1
package/dist/mcp/server.js +14 -8
package/dist/mcp/server.js.map +1 -1
package/dist/mcp/tool-registry.d.ts +1 -1
package/dist/mcp/tool-registry.d.ts.map +1 -1
package/dist/mcp/tool-registry.js +23 -5
package/dist/mcp/tool-registry.js.map +1 -1
package/dist/mcp/tools/semantic-search.d.ts +1 -0
package/dist/mcp/tools/semantic-search.d.ts.map +1 -1
package/dist/mcp/tools/semantic-search.js +1 -0
package/dist/mcp/tools/semantic-search.js.map +1 -1
package/dist/types.d.ts +16 -1
package/dist/types.d.ts.map +1 -1
package/grammars/tree-sitter-erlang.wasm +0 -0
package/grammars/tree-sitter-fsharp.wasm +0 -0
package/grammars/tree-sitter-fsharp_signature.wasm +0 -0
package/grammars/tree-sitter-gleam.wasm +0 -0
package/package.json +11 -10
package/src/ast-analysis/engine.ts +3 -1
package/src/ast-analysis/rules/index.ts +87 -0
package/src/ast-analysis/visitors/ast-store-visitor.ts +45 -9
package/src/cli/commands/audit.ts +1 -1
package/src/cli/commands/build.ts +2 -0
package/src/cli/commands/check.ts +1 -1
package/src/cli/commands/children.ts +1 -1
package/src/cli/commands/diff-impact.ts +1 -1
package/src/cli/commands/roles.ts +1 -1
package/src/cli/commands/structure.ts +1 -1
package/src/cli/shared/options.ts +1 -1
package/src/db/connection.ts +8 -0
package/src/domain/graph/builder/context.ts +10 -0
package/src/domain/graph/builder/helpers.ts +8 -3
package/src/domain/graph/builder/incremental.ts +6 -41
package/src/domain/graph/builder/pipeline.ts +404 -41
package/src/domain/graph/builder/stages/build-edges.ts +9 -2
package/src/domain/graph/builder/stages/collect-files.ts +9 -0
package/src/domain/graph/builder/stages/detect-changes.ts +130 -4
package/src/domain/graph/builder/stages/finalize.ts +9 -6
package/src/domain/graph/builder/stages/insert-nodes.ts +38 -14
package/src/domain/graph/builder/stages/resolve-imports.ts +79 -25
package/src/domain/graph/watcher.ts +21 -23
package/src/domain/parser.ts +110 -10
package/src/domain/search/models.ts +37 -2
package/src/domain/wasm-worker-entry.ts +20 -13
package/src/extractors/c.ts +27 -8
package/src/extractors/cpp.ts +50 -8
package/src/extractors/cuda.ts +90 -16
package/src/extractors/elixir.ts +75 -3
package/src/extractors/erlang.ts +63 -20
package/src/extractors/fsharp.ts +104 -0
package/src/extractors/gleam.ts +7 -2
package/src/extractors/groovy.ts +45 -1
package/src/extractors/haskell.ts +45 -4
package/src/extractors/julia.ts +164 -43
package/src/extractors/kotlin.ts +4 -0
package/src/extractors/objc.ts +171 -47
package/src/extractors/python.ts +5 -3
package/src/extractors/r.ts +88 -48
package/src/extractors/scala.ts +24 -36
package/src/extractors/solidity.ts +17 -8
package/src/extractors/verilog.ts +83 -15
package/src/infrastructure/config.ts +1 -0
package/src/mcp/server.ts +16 -9
package/src/mcp/tool-registry.ts +28 -5
package/src/mcp/tools/semantic-search.ts +2 -0
package/src/types.ts +16 -0

package/dist/cli/commands/children.js.map CHANGED Viewed

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package/dist/cli/commands/diff-impact.js CHANGED Viewed

@@ -6,7 +6,7 @@ export const command = {
         ['-d, --db <path>', 'Path to graph.db'],
         ['-T, --no-tests', 'Exclude test/spec files from results'],
         ['--include-tests', 'Include test/spec files (overrides excludeTests config)'],
-        ['--limit <number>', 'Max results to return'],
+        ['-n, --limit <number>', 'Max results to return'],
         ['--offset <number>', 'Skip N results (default: 0)'],
         ['--ndjson', 'Newline-delimited JSON output'],
         ['--staged', 'Analyze staged changes instead of unstaged'],

package/dist/cli/commands/diff-impact.js.map CHANGED Viewed

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package/dist/cli/commands/roles.js CHANGED Viewed

@@ -11,7 +11,7 @@ export const command = {
         ['-T, --no-tests', 'Exclude test/spec files'],
         ['--include-tests', 'Include test/spec files (overrides excludeTests config)'],
         ['-j, --json', 'Output as JSON'],
-        ['--limit <number>', 'Max results to return'],
+        ['-n, --limit <number>', 'Max results to return'],
         ['--offset <number>', 'Skip N results (default: 0)'],
         ['--ndjson', 'Newline-delimited JSON output'],
     ],

package/dist/cli/commands/roles.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"roles.js","sourceRoot":"","sources":["../../../src/cli/commands/roles.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,2BAA2B,CAAC;AACxD,OAAO,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AACtD,OAAO,EAAE,KAAK,EAAE,MAAM,mCAAmC,CAAC;AAG1D,MAAM,CAAC,MAAM,OAAO,GAAsB;IACxC,IAAI,EAAE,OAAO;IACb,WAAW,EACT,6HAA6H;IAC/H,OAAO,EAAE;QACP,CAAC,iBAAiB,EAAE,kBAAkB,CAAC;QACvC,CAAC,eAAe,EAAE,mBAAmB,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC;QAC/D,CAAC,mBAAmB,EAAE,sDAAsD,EAAE,WAAW,CAAC;QAC1F,CAAC,gBAAgB,EAAE,yBAAyB,CAAC;QAC7C,CAAC,iBAAiB,EAAE,yDAAyD,CAAC;QAC9E,CAAC,YAAY,EAAE,gBAAgB,CAAC;QAChC,CAAC,sBAAsB,EAAE,uBAAuB,CAAC;QACjD,CAAC,mBAAmB,EAAE,6BAA6B,CAAC;QACpD,CAAC,UAAU,EAAE,+BAA+B,CAAC;KAC9C;IACD,QAAQ,CAAC,KAAK,EAAE,IAAI;QAClB,IAAI,IAAI,CAAC,IAAI,IAAI,CAAE,WAAiC,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACzE,OAAO,iBAAiB,IAAI,CAAC,IAAI,mBAAmB,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;QAC/E,CAAC;IACH,CAAC;IACD,OAAO,CAAC,KAAK,EAAE,IAAI,EAAE,GAAG;QACtB,KAAK,CAAC,IAAI,CAAC,EAAE,EAAE;YACb,IAAI,EAAE,IAAI,CAAC,IAAI;YACf,IAAI,EAAE,IAAI,CAAC,IAAI;YACf,GAAG,GAAG,CAAC,gBAAgB,CAAC,IAAI,CAAC;SAC9B,CAAC,CAAC;IACL,CAAC;CACF,CAAC"}

package/dist/cli/commands/structure.js CHANGED Viewed

@@ -9,7 +9,7 @@ export const command = {
         ['-T, --no-tests', 'Exclude test/spec files'],
         ['--include-tests', 'Include test/spec files (overrides excludeTests config)'],
         ['-j, --json', 'Output as JSON'],
-        ['--limit <number>', 'Max results to return'],
+        ['-n, --limit <number>', 'Max results to return'],
         ['--offset <number>', 'Skip N results (default: 0)'],
         ['--ndjson', 'Newline-delimited JSON output'],
         ['--modules', 'Show module boundaries (directories with high cohesion)'],

package/dist/cli/commands/structure.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"structure.js","sourceRoot":"","sources":["../../../src/cli/commands/structure.ts"],"names":[],"mappings":"AAEA,MAAM,CAAC,MAAM,OAAO,GAAsB;IACxC,IAAI,EAAE,iBAAiB;IACvB,WAAW,EACT,wFAAwF;IAC1F,OAAO,EAAE;QACP,CAAC,iBAAiB,EAAE,kBAAkB,CAAC;QACvC,CAAC,aAAa,EAAE,qBAAqB,CAAC;QACtC,CAAC,iBAAiB,EAAE,wDAAwD,EAAE,OAAO,CAAC;QACtF,CAAC,QAAQ,EAAE,8BAA8B,CAAC;QAC1C,CAAC,gBAAgB,EAAE,yBAAyB,CAAC;QAC7C,CAAC,iBAAiB,EAAE,yDAAyD,CAAC;QAC9E,CAAC,YAAY,EAAE,gBAAgB,CAAC;QAChC,CAAC,~~kBAAkB~~,EAAE,uBAAuB,CAAC;~~QAC7C~~,CAAC,mBAAmB,EAAE,6BAA6B,CAAC;QACpD,CAAC,UAAU,EAAE,+BAA+B,CAAC;QAC7C,CAAC,WAAW,EAAE,yDAAyD,CAAC;QACxE,CAAC,sBAAsB,EAAE,iDAAiD,CAAC;KAC5E;IACD,KAAK,CAAC,OAAO,CAAC,CAAC,GAAG,CAAC,EAAE,IAAI,EAAE,GAAG;QAC5B,MAAM,EAAE,aAAa,EAAE,eAAe,EAAE,oBAAoB,EAAE,sBAAsB,EAAE,GACpF,MAAM,MAAM,CAAC,iCAAiC,CAAC,CAAC;QAElD,IAAI,IAAI,CAAC,OAAO,EAAE,CAAC;YACjB,MAAM,MAAM,GAAG,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,UAAU,CAAC,IAAI,CAAC,SAAmB,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC;YACjF,IAAI,MAAM,KAAK,SAAS,IAAI,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,EAAE,CAAC;gBACjD,OAAO,CAAC,KAAK,CAAC,qCAAqC,CAAC,CAAC;gBACrD,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;gBACrB,OAAO;YACT,CAAC;YACD,MAAM,IAAI,GAAG,oBAAoB,CAAC,IAAI,CAAC,EAAE,EAAE;gBACzC,SAAS,EAAE,MAAM;aAClB,CAAC,CAAC;YACH,IAAI,CAAC,GAAG,CAAC,YAAY,CAAC,IAAI,EAAE,SAAS,EAAE,IAAI,CAAC,EAAE,CAAC;gBAC7C,OAAO,CAAC,GAAG,CAAC,sBAAsB,CAAC,IAAI,CAAC,CAAC,CAAC;YAC5C,CAAC;YACD,OAAO;QACT,CAAC;QAED,MAAM,KAAK,GAAG,GAAG,CAAC,gBAAgB,CAAC,IAAI,CAAC,CAAC;QACzC,MAAM,IAAI,GAAG,aAAa,CAAC,IAAI,CAAC,EAAE,EAAE;YAClC,SAAS,EAAE,GAAG;YACd,KAAK,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,KAAe,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YAClE,IAAI,EAAE,IAAI,CAAC,IAAI;YACf,IAAI,EAAE,IAAI,CAAC,IAAI;YACf,OAAO,EAAE,KAAK,CAAC,OAAO;YACtB,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,MAAM,EAAE,KAAK,CAAC,MAAM;SACrB,CAAC,CAAC;QACH,IAAI,CAAC,GAAG,CAAC,YAAY,CAAC,IAAI,EAAE,aAAa,EAAE,IAAI,CAAC,EAAE,CAAC;YACjD,OAAO,CAAC,GAAG,CAAC,eAAe,CAAC,IAAI,CAAC,CAAC,CAAC;QACrC,CAAC;IACH,CAAC;CACF,CAAC"}
1	+ {"version":3,"file":"structure.js","sourceRoot":"","sources":["../../../src/cli/commands/structure.ts"],"names":[],"mappings":"AAEA,MAAM,CAAC,MAAM,OAAO,GAAsB;IACxC,IAAI,EAAE,iBAAiB;IACvB,WAAW,EACT,wFAAwF;IAC1F,OAAO,EAAE;QACP,CAAC,iBAAiB,EAAE,kBAAkB,CAAC;QACvC,CAAC,aAAa,EAAE,qBAAqB,CAAC;QACtC,CAAC,iBAAiB,EAAE,wDAAwD,EAAE,OAAO,CAAC;QACtF,CAAC,QAAQ,EAAE,8BAA8B,CAAC;QAC1C,CAAC,gBAAgB,EAAE,yBAAyB,CAAC;QAC7C,CAAC,iBAAiB,EAAE,yDAAyD,CAAC;QAC9E,CAAC,YAAY,EAAE,gBAAgB,CAAC;QAChC,CAAC,sBAAsB,EAAE,uBAAuB,CAAC;QACjD,CAAC,mBAAmB,EAAE,6BAA6B,CAAC;QACpD,CAAC,UAAU,EAAE,+BAA+B,CAAC;QAC7C,CAAC,WAAW,EAAE,yDAAyD,CAAC;QACxE,CAAC,sBAAsB,EAAE,iDAAiD,CAAC;KAC5E;IACD,KAAK,CAAC,OAAO,CAAC,CAAC,GAAG,CAAC,EAAE,IAAI,EAAE,GAAG;QAC5B,MAAM,EAAE,aAAa,EAAE,eAAe,EAAE,oBAAoB,EAAE,sBAAsB,EAAE,GACpF,MAAM,MAAM,CAAC,iCAAiC,CAAC,CAAC;QAElD,IAAI,IAAI,CAAC,OAAO,EAAE,CAAC;YACjB,MAAM,MAAM,GAAG,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,UAAU,CAAC,IAAI,CAAC,SAAmB,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC;YACjF,IAAI,MAAM,KAAK,SAAS,IAAI,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,EAAE,CAAC;gBACjD,OAAO,CAAC,KAAK,CAAC,qCAAqC,CAAC,CAAC;gBACrD,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAC;gBACrB,OAAO;YACT,CAAC;YACD,MAAM,IAAI,GAAG,oBAAoB,CAAC,IAAI,CAAC,EAAE,EAAE;gBACzC,SAAS,EAAE,MAAM;aAClB,CAAC,CAAC;YACH,IAAI,CAAC,GAAG,CAAC,YAAY,CAAC,IAAI,EAAE,SAAS,EAAE,IAAI,CAAC,EAAE,CAAC;gBAC7C,OAAO,CAAC,GAAG,CAAC,sBAAsB,CAAC,IAAI,CAAC,CAAC,CAAC;YAC5C,CAAC;YACD,OAAO;QACT,CAAC;QAED,MAAM,KAAK,GAAG,GAAG,CAAC,gBAAgB,CAAC,IAAI,CAAC,CAAC;QACzC,MAAM,IAAI,GAAG,aAAa,CAAC,IAAI,CAAC,EAAE,EAAE;YAClC,SAAS,EAAE,GAAG;YACd,KAAK,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,KAAe,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YAClE,IAAI,EAAE,IAAI,CAAC,IAAI;YACf,IAAI,EAAE,IAAI,CAAC,IAAI;YACf,OAAO,EAAE,KAAK,CAAC,OAAO;YACtB,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,MAAM,EAAE,KAAK,CAAC,MAAM;SACrB,CAAC,CAAC;QACH,IAAI,CAAC,GAAG,CAAC,YAAY,CAAC,IAAI,EAAE,aAAa,EAAE,IAAI,CAAC,EAAE,CAAC;YACjD,OAAO,CAAC,GAAG,CAAC,eAAe,CAAC,IAAI,CAAC,CAAC,CAAC;QACrC,CAAC;IACH,CAAC;CACF,CAAC"}

package/dist/cli/shared/options.js CHANGED Viewed

@@ -9,7 +9,7 @@ export function applyQueryOpts(cmd) {
         .option('-T, --no-tests', 'Exclude test/spec files from results')
         .option('--include-tests', 'Include test/spec files (overrides excludeTests config)')
         .option('-j, --json', 'Output as JSON')
-        .option('--limit <number>', 'Max results to return')
+        .option('-n, --limit <number>', 'Max results to return')
         .option('--offset <number>', 'Skip N results (default: 0)')
         .option('--ndjson', 'Newline-delimited JSON output')
         .option('--table', 'Output as aligned table')

package/dist/cli/shared/options.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/db/connection.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/db/connection.js CHANGED Viewed

@@ -280,6 +280,14 @@ export function findDbPath(customPath) {
             debug(`findDbPath: stopped at git ceiling ${ceiling}`);
             break;
         }
+        // Outside a git repo, cwd is the first (and only) directory we'll check.
+        // Walking past it risks attaching to a stale .codegraph/ in an unrelated
+        // parent — e.g. /private/tmp/.codegraph/ leaking into every /tmp/foo/ run,
+        // or $HOME/.codegraph/ leaking into every scratch dir under $HOME.
+        if (!ceiling) {
+            debug(`findDbPath: no git ceiling, stopping at ${dir}`);
+            break;
+        }
         const parent = path.dirname(dir);
         if (parent === dir)
             break;

package/dist/db/connection.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/domain/graph/builder/context.d.ts CHANGED Viewed

@@ -14,6 +14,16 @@ export declare class PipelineContext {
     engineOpts: EngineOpts;
     engineName: 'native' | 'wasm';
     engineVersion: string | null;
+    /**
+     * The version reported by the native binary itself (CARGO_PKG_VERSION at
+     * build time), as opposed to `engineVersion` which prefers the platform
+     * package.json. The Rust orchestrator's check_version_mismatch compares
+     * `build_meta.engine_version` against CARGO_PKG_VERSION, so build_meta
+     * writes must use this value to avoid a perpetual full-rebuild loop when
+     * the binary and platform package.json drift apart (e.g., CI hot-swap
+     * via ci-install-native.mjs — #1066).
+     */
+    nativeBinaryVersion: string | null;
     aliases: PathAliases;
     incremental: boolean;
     forceFullRebuild: boolean;

package/dist/domain/graph/builder/context.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/domain/graph/builder/context.js CHANGED Viewed

@@ -8,6 +8,16 @@ export class PipelineContext {
     engineOpts;
     engineName;
     engineVersion;
+    /**
+     * The version reported by the native binary itself (CARGO_PKG_VERSION at
+     * build time), as opposed to `engineVersion` which prefers the platform
+     * package.json. The Rust orchestrator's check_version_mismatch compares
+     * `build_meta.engine_version` against CARGO_PKG_VERSION, so build_meta
+     * writes must use this value to avoid a perpetual full-rebuild loop when
+     * the binary and platform package.json drift apart (e.g., CI hot-swap
+     * via ci-install-native.mjs — #1066).
+     */
+    nativeBinaryVersion;
     aliases;
     incremental;
     forceFullRebuild = false;

package/dist/domain/graph/builder/context.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"context.js","sourceRoot":"","sources":["../../../../src/domain/graph/builder/context.ts"],"names":[],"mappings":"AAoBA,MAAM,OAAO,eAAe;IAC1B,sEAAsE;IACtE,OAAO,CAAU;IACjB,EAAE,CAAyB;IAC3B,MAAM,CAAU;IAChB,MAAM,CAAmB;IACzB,IAAI,CAAkB;IACtB,UAAU,CAAc;IACxB,UAAU,CAAqB;IAC/B,aAAa,CAAiB;IAC9B,OAAO,CAAe;IACtB,WAAW,CAAW;IACtB,gBAAgB,GAAY,KAAK,CAAC;IAClC,aAAa,CAAU;IACvB,QAAQ,CAAkB;IAC1B,kFAAkF;IAClF,eAAe,GAAY,KAAK,CAAC;IACjC,gGAAgG;IAChG,gBAAgB,GAAY,KAAK,CAAC;IAElC,sEAAsE;IACtE,QAAQ,CAAY;IACpB,cAAc,CAAe;IAE7B,sEAAsE;IACtE,WAAW,CAAW;IACtB,YAAY,CAAiB;IAC7B,eAAe,CAAoB;IACnC,OAAO,CAAY;IACnB,SAAS,GAAY,KAAK,CAAC;IAE3B,sEAAsE;IACtE,UAAU,CAAgC;IAC1C,WAAW,CAAgC;IAC3C,YAAY,CAAiB;IAE7B,sEAAsE;IACtE,aAAa,CAA8B;IAC3C,WAAW,CAA0B;IACrC,eAAe,CAAe;IAE9B,sEAAsE;IACtE,WAAW,CAA0B;IACrC,kBAAkB,CAA0B;IAE5C,sEAAsE;IACtE;;;;OAIG;IACH,oBAAoB,GASf,EAAE,CAAC;IAER,sEAAsE;IACtE,aAAa,GAAY,KAAK,CAAC;IAC/B,YAAY,CAAuB;IAEnC,sEAAsE;IACtE,MAAM,GAgBF,EAAE,CAAC;IACP,UAAU,CAAU;CACrB"}
1	+ {"version":3,"file":"context.js","sourceRoot":"","sources":["../../../../src/domain/graph/builder/context.ts"],"names":[],"mappings":"AAoBA,MAAM,OAAO,eAAe;IAC1B,sEAAsE;IACtE,OAAO,CAAU;IACjB,EAAE,CAAyB;IAC3B,MAAM,CAAU;IAChB,MAAM,CAAmB;IACzB,IAAI,CAAkB;IACtB,UAAU,CAAc;IACxB,UAAU,CAAqB;IAC/B,aAAa,CAAiB;IAC9B;;;;;;;;OAQG;IACH,mBAAmB,CAAiB;IACpC,OAAO,CAAe;IACtB,WAAW,CAAW;IACtB,gBAAgB,GAAY,KAAK,CAAC;IAClC,aAAa,CAAU;IACvB,QAAQ,CAAkB;IAC1B,kFAAkF;IAClF,eAAe,GAAY,KAAK,CAAC;IACjC,gGAAgG;IAChG,gBAAgB,GAAY,KAAK,CAAC;IAElC,sEAAsE;IACtE,QAAQ,CAAY;IACpB,cAAc,CAAe;IAE7B,sEAAsE;IACtE,WAAW,CAAW;IACtB,YAAY,CAAiB;IAC7B,eAAe,CAAoB;IACnC,OAAO,CAAY;IACnB,SAAS,GAAY,KAAK,CAAC;IAE3B,sEAAsE;IACtE,UAAU,CAAgC;IAC1C,WAAW,CAAgC;IAC3C,YAAY,CAAiB;IAE7B,sEAAsE;IACtE,aAAa,CAA8B;IAC3C,WAAW,CAA0B;IACrC,eAAe,CAAe;IAE9B,sEAAsE;IACtE,WAAW,CAA0B;IACrC,kBAAkB,CAA0B;IAE5C,sEAAsE;IACtE;;;;OAIG;IACH,oBAAoB,GASf,EAAE,CAAC;IAER,sEAAsE;IACtE,aAAa,GAAY,KAAK,CAAC;IAC/B,YAAY,CAAuB;IAEnC,sEAAsE;IACtE,MAAM,GAgBF,EAAE,CAAC;IACP,UAAU,CAAU;CACrB"}

package/dist/domain/graph/builder/helpers.d.ts CHANGED Viewed

@@ -29,10 +29,15 @@ export declare function loadPathAliases(rootDir: string): PathAliases;
  */
 export declare function fileHash(content: string): string;
 /**
- * Stat a file, returning { mtimeMs, size } or null on error.
+ * Stat a file, returning { mtime, size } or null on error.
+ *
+ * `mtime` is `Math.floor(stat.mtimeMs)` so it matches the integer column
+ * stored in the DB. Floor-once-here keeps every consumer honest: storing or
+ * comparing a non-floored `mtimeMs` against the integer DB column would cause
+ * spurious fast-skip misses on the next build.
  */
 export declare function fileStat(filePath: string): {
-    mtimeMs: number;
+    mtime: number;
     size: number;
 } | null;
 export declare function readFileSafe(filePath: string, retries?: number): string;

package/dist/domain/graph/builder/helpers.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"helpers.d.ts","sourceRoot":"","sources":["../../../../src/domain/graph/builder/helpers.ts"],"names":[],"mappings":"AAYA,OAAO,KAAK,EACV,qBAAqB,EACrB,eAAe,EACf,WAAW,EAEZ,MAAM,mBAAmB,CAAC;AAE3B,eAAO,MAAM,iBAAiB,EAAE,GAAG,CAAC,MAAM,CA6BxC,CAAC;AAaH;;;;;;GAMG;AACH,wBAAgB,oBAAoB,CAClC,OAAO,EAAE,MAAM,EACf,cAAc,EAAE,SAAS,MAAM,EAAE,EACjC,cAAc,EAAE,SAAS,MAAM,EAAE,GAChC,OAAO,CAIT;AAED;;;;;;GAMG;AACH,wBAAgB,YAAY,CAC1B,GAAG,EAAE,MAAM,EACX,KAAK,EAAE,MAAM,EAAE,EACf,MAAM,EAAE,OAAO,CAAC,eAAe,CAAC,EAChC,WAAW,EAAE,GAAG,CAAC,MAAM,CAAC,EACxB,QAAQ,CAAC,EAAE,GAAG,CAAC,MAAM,CAAC,EACtB,QAAQ,CAAC,EAAE,MAAM,EACjB,eAAe,CAAC,EAAE,SAAS,MAAM,EAAE,EACnC,eAAe,CAAC,EAAE,SAAS,MAAM,EAAE,GAClC;IAAE,KAAK,EAAE,MAAM,EAAE,CAAC;IAAC,WAAW,EAAE,GAAG,CAAC,MAAM,CAAC,CAAA;CAAE,CAAC;AACjD,wBAAgB,YAAY,CAC1B,GAAG,EAAE,MAAM,EACX,KAAK,CAAC,EAAE,MAAM,EAAE,EAChB,MAAM,CAAC,EAAE,OAAO,CAAC,eAAe,CAAC,EACjC,WAAW,CAAC,EAAE,IAAI,EAClB,QAAQ,CAAC,EAAE,GAAG,CAAC,MAAM,CAAC,EACtB,QAAQ,CAAC,EAAE,MAAM,EACjB,eAAe,CAAC,EAAE,SAAS,MAAM,EAAE,EACnC,eAAe,CAAC,EAAE,SAAS,MAAM,EAAE,GAClC,MAAM,EAAE,CAAC;AA+EZ;;GAEG;AACH,wBAAgB,eAAe,CAAC,OAAO,EAAE,MAAM,GAAG,WAAW,CA4B5D;AAED;;GAEG;AACH,wBAAgB,QAAQ,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,CAEhD;AAED~~;;GAEG~~;AACH,wBAAgB,QAAQ,CAAC,QAAQ,EAAE,MAAM,GAAG;IAAE,~~OAAO~~,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,GAAG,IAAI,~~CAOnF~~;AAQD,wBAAgB,YAAY,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,GAAE,MAAU,GAAG,MAAM,CAa1E;AAED;;GAEG;AACH,wBAAgB,mBAAmB,CACjC,EAAE,EAAE,qBAAqB,EACzB,KAAK,EAAE,MAAM,EAAE,EACf,OAAO,GAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAM,GACpC,IAAI,CAGN;AA6CD;;;GAGG;AACH,wBAAgB,gBAAgB,CAAC,EAAE,EAAE,qBAAqB,EAAE,IAAI,EAAE,OAAO,EAAE,EAAE,GAAG,IAAI,CAanF;AAED;;;GAGG;AACH,wBAAgB,gBAAgB,CAAC,EAAE,EAAE,qBAAqB,EAAE,IAAI,EAAE,OAAO,EAAE,EAAE,GAAG,IAAI,CAanF"}
1	+ {"version":3,"file":"helpers.d.ts","sourceRoot":"","sources":["../../../../src/domain/graph/builder/helpers.ts"],"names":[],"mappings":"AAYA,OAAO,KAAK,EACV,qBAAqB,EACrB,eAAe,EACf,WAAW,EAEZ,MAAM,mBAAmB,CAAC;AAE3B,eAAO,MAAM,iBAAiB,EAAE,GAAG,CAAC,MAAM,CA6BxC,CAAC;AAaH;;;;;;GAMG;AACH,wBAAgB,oBAAoB,CAClC,OAAO,EAAE,MAAM,EACf,cAAc,EAAE,SAAS,MAAM,EAAE,EACjC,cAAc,EAAE,SAAS,MAAM,EAAE,GAChC,OAAO,CAIT;AAED;;;;;;GAMG;AACH,wBAAgB,YAAY,CAC1B,GAAG,EAAE,MAAM,EACX,KAAK,EAAE,MAAM,EAAE,EACf,MAAM,EAAE,OAAO,CAAC,eAAe,CAAC,EAChC,WAAW,EAAE,GAAG,CAAC,MAAM,CAAC,EACxB,QAAQ,CAAC,EAAE,GAAG,CAAC,MAAM,CAAC,EACtB,QAAQ,CAAC,EAAE,MAAM,EACjB,eAAe,CAAC,EAAE,SAAS,MAAM,EAAE,EACnC,eAAe,CAAC,EAAE,SAAS,MAAM,EAAE,GAClC;IAAE,KAAK,EAAE,MAAM,EAAE,CAAC;IAAC,WAAW,EAAE,GAAG,CAAC,MAAM,CAAC,CAAA;CAAE,CAAC;AACjD,wBAAgB,YAAY,CAC1B,GAAG,EAAE,MAAM,EACX,KAAK,CAAC,EAAE,MAAM,EAAE,EAChB,MAAM,CAAC,EAAE,OAAO,CAAC,eAAe,CAAC,EACjC,WAAW,CAAC,EAAE,IAAI,EAClB,QAAQ,CAAC,EAAE,GAAG,CAAC,MAAM,CAAC,EACtB,QAAQ,CAAC,EAAE,MAAM,EACjB,eAAe,CAAC,EAAE,SAAS,MAAM,EAAE,EACnC,eAAe,CAAC,EAAE,SAAS,MAAM,EAAE,GAClC,MAAM,EAAE,CAAC;AA+EZ;;GAEG;AACH,wBAAgB,eAAe,CAAC,OAAO,EAAE,MAAM,GAAG,WAAW,CA4B5D;AAED;;GAEG;AACH,wBAAgB,QAAQ,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,CAEhD;AAED;;;;;;;GAOG;AACH,wBAAgB,QAAQ,CAAC,QAAQ,EAAE,MAAM,GAAG;IAAE,KAAK,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,GAAG,IAAI,CAOjF;AAQD,wBAAgB,YAAY,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,GAAE,MAAU,GAAG,MAAM,CAa1E;AAED;;GAEG;AACH,wBAAgB,mBAAmB,CACjC,EAAE,EAAE,qBAAqB,EACzB,KAAK,EAAE,MAAM,EAAE,EACf,OAAO,GAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAM,GACpC,IAAI,CAGN;AA6CD;;;GAGG;AACH,wBAAgB,gBAAgB,CAAC,EAAE,EAAE,qBAAqB,EAAE,IAAI,EAAE,OAAO,EAAE,EAAE,GAAG,IAAI,CAanF;AAED;;;GAGG;AACH,wBAAgB,gBAAgB,CAAC,EAAE,EAAE,qBAAqB,EAAE,IAAI,EAAE,OAAO,EAAE,EAAE,GAAG,IAAI,CAanF"}

package/dist/domain/graph/builder/helpers.js CHANGED Viewed

@@ -165,12 +165,17 @@ export function fileHash(content) {
     return createHash('md5').update(content).digest('hex');
 }
 /**
- * Stat a file, returning { mtimeMs, size } or null on error.
+ * Stat a file, returning { mtime, size } or null on error.
+ *
+ * `mtime` is `Math.floor(stat.mtimeMs)` so it matches the integer column
+ * stored in the DB. Floor-once-here keeps every consumer honest: storing or
+ * comparing a non-floored `mtimeMs` against the integer DB column would cause
+ * spurious fast-skip misses on the next build.
  */
 export function fileStat(filePath) {
     try {
         const s = fs.statSync(filePath);
-        return { mtimeMs: s.mtimeMs, size: s.size };
+        return { mtime: Math.floor(s.mtimeMs), size: s.size };
     }
     catch {
         return null;

package/dist/domain/graph/builder/helpers.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/domain/graph/builder/incremental.d.ts CHANGED Viewed

@@ -11,12 +11,6 @@ export interface IncrementalStmts {
             id: number;
         } | undefined;
     };
-    deleteEdgesForFile: {
-        run: (...params: unknown[]) => unknown;
-    };
-    deleteNodes: {
-        run: (...params: unknown[]) => unknown;
-    };
     countNodes: {
         get: (...params: unknown[]) => {
             c: number;

package/dist/domain/graph/builder/incremental.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/domain/graph/builder/incremental.js CHANGED Viewed

@@ -9,7 +9,7 @@
  */
 import fs from 'node:fs';
 import path from 'node:path';
-import { bulkNodeIdsByFile } from '../../../db/index.js';
+import { bulkNodeIdsByFile, purgeFileData } from '../../../db/index.js';
 import { debug, warn } from '../../../infrastructure/logger.js';
 import { normalizePath } from '../../../shared/constants.js';
 import { parseFileIncremental } from '../../parser.js';
@@ -126,24 +126,6 @@ function rebuildDirContainment(_db, stmts, relPath) {
     }
     return 0;
 }
-// ── Ancillary table cleanup ────────────────────────────────────────────
-function purgeAncillaryData(db, relPath) {
-    const tryExec = (sql, ...args) => {
-        try {
-            db.prepare(sql).run(...args);
-        }
-        catch (err) {
-            if (!err?.message?.includes('no such table'))
-                throw err;
-        }
-    };
-    tryExec('DELETE FROM function_complexity WHERE node_id IN (SELECT id FROM nodes WHERE file = ?)', relPath);
-    tryExec('DELETE FROM node_metrics WHERE node_id IN (SELECT id FROM nodes WHERE file = ?)', relPath);
-    tryExec('DELETE FROM cfg_edges WHERE function_node_id IN (SELECT id FROM nodes WHERE file = ?)', relPath);
-    tryExec('DELETE FROM cfg_blocks WHERE function_node_id IN (SELECT id FROM nodes WHERE file = ?)', relPath);
-    tryExec('DELETE FROM dataflow WHERE source_id IN (SELECT id FROM nodes WHERE file = ?) OR target_id IN (SELECT id FROM nodes WHERE file = ?)', relPath, relPath);
-    tryExec('DELETE FROM ast_nodes WHERE file = ?', relPath);
-}
 // ── Import edge building ────────────────────────────────────────────────
 // Lazily-cached prepared statements for barrel resolution (avoid re-preparing in hot loops)
 let _barrelDb = null;
@@ -348,10 +330,11 @@ export async function rebuildFile(db, rootDir, filePath, stmts, engineOpts, cach
     const oldSymbols = diffSymbols ? stmts.listSymbols.all(relPath) : [];
     // Find reverse-deps BEFORE purging (edges still reference the old nodes)
     const reverseDeps = findReverseDeps(db, relPath);
-    // Purge ancillary tables, then edges, then nodes
-    purgeAncillaryData(db, relPath);
-    stmts.deleteEdgesForFile.run(relPath);
-    stmts.deleteNodes.run(relPath);
+    // Purge ancillary tables (incl. embeddings), edges, and nodes in one pass.
+    // Embeddings must be purged before nodes — better-sqlite3 enforces foreign
+    // keys by default, and `embeddings.node_id` references `nodes.id`. Issue #1176.
+    // `purgeHashes: false` preserves file_hashes for the next incremental build.
+    purgeFileData(db, relPath, { purgeHashes: false });
     if (!fs.existsSync(filePath)) {
         if (cache)
             cache.remove(filePath);

package/dist/domain/graph/builder/incremental.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/domain/graph/builder/pipeline.d.ts CHANGED Viewed

@@ -1,4 +1,48 @@
 import type { BuildGraphOpts, BuildResult } from '../../../types.js';
+/**
+ * Inputs to {@link computeWasmOnlyStaleFiles}. Sets are passed in so the helper
+ * is pure and unit-testable independently of `getInstalledWasmExtensions` and
+ * the `NATIVE_SUPPORTED_EXTENSIONS` global state.
+ */
+export interface WasmOnlyStaleFilesInput {
+    /** Distinct `file` values from the `nodes` table. */
+    existingNodes: ReadonlySet<string>;
+    /** Distinct `file` values from the `file_hashes` table. */
+    existingHashes: ReadonlySet<string>;
+    /** Relative paths currently on disk (from `collectFilesUtil`). */
+    expected: ReadonlySet<string>;
+    /** Lowercased extensions whose WASM grammar is installed. */
+    installedExts: ReadonlySet<string>;
+    /** Extensions covered by the Rust addon — Rust owns deletion for these. */
+    nativeSupported: ReadonlySet<string>;
+}
+/**
+ * Compute the WASM-only files present in the DB but missing from disk (#1073).
+ *
+ * Returns relative paths that:
+ *   - appear in `existingNodes` or `existingHashes` (in DB),
+ *   - are absent from `expected` (not on disk),
+ *   - have an extension installed for WASM, AND
+ *   - have an extension NOT covered by `nativeSupported` — Rust's
+ *     `purge_changed_files` handles deletion for natively-supported extensions
+ *     via its own `detect_removed_files`, so the caller must not double-purge.
+ *
+ * Extensions are lowercased before lookup to match the registry and Rust's
+ * `LanguageKind::from_extension` (which normalises case for the languages
+ * where both cases are conventional, e.g. R's `.r` / `.R`).
+ *
+ * DB paths are forced to forward slashes before comparison with `expected`
+ * (which is always normalised). The on-disk invariant is that DB rows are
+ * written with forward slashes, but a stale row written by older code on
+ * Windows could carry back-slashes — normalising here makes the comparison
+ * platform-safe and prevents false-positive purges of live rows. We replace
+ * `\\` explicitly (rather than calling `normalizePath`, which only touches
+ * `path.sep`) so the defence works when running on POSIX against a DB that
+ * was migrated from Windows.
+ *
+ * Exported for unit testing.
+ */
+export declare function computeWasmOnlyStaleFiles(input: WasmOnlyStaleFilesInput): string[];
 /**
  * Build the dependency graph for a codebase.
  *

package/dist/domain/graph/builder/pipeline.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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