AFT issue: After upgrading AFT from 0.56.0 to 0.56.1, semantic search times out on

Description

After upgrading AFT from 0.56.0 to 0.56.1, semantic search times out on multi-word queries (60s timeout) or fails with "search_engine_failed - re-verification of live memo entry at epoch 0 is rejected". Exact-match single-word searches work fine. npx aft doctor shows all indexes ready (Search Index: 2K files 21.4MB, Semantic Index: 4K entries 7.8MB). Semantic engine appears broken despite healthy index status.

Environment

AFT CLI: v0.56.1
AFT binary: 0.56.1
OS: linux x64
Node: v26.3.0
Session: ses_f50a5ff64ffeNUAkYtA87ImyuE (Retry search query after timeout)

Diagnostics

Timestamp: 2026-09-17T13:19:07.939Z
AFT CLI: v0.56.1
AFT binary: 0.56.1
OS: linux x64
Node: v26.3.0

OpenCode

Host installed: true
Host version: 1.18.31
Plugin registered: true
Plugin version: 0.56.1
AFT enabled: true
AFT config parse error: none

Config paths

{
  "configDir": "~/.config/opencode",
  "harnessConfig": "~/.config/opencode/opencode.json",
  "harnessConfigFormat": "json",
  "aftConfig": "~/.config/cortexkit/aft.jsonc",
  "aftConfigFormat": "jsonc",
  "tuiConfig": "~/.config/opencode/tui.jsonc",
  "tuiConfigFormat": "jsonc"
}

AFT flags

{
  "$schema": "https://raw.githubusercontent.com/cortexkit/aft/main/assets/aft.schema.json",
  "search_index": true,
  "semantic_search": true,
  "tool_surface": "all",
  "format_on_edit": true
}

Plugin cache

{
  "path": "~/.cache/opencode/packages/@cortexkit/aft-opencode@0.56.1",
  "cached": "0.56.1",
  "latest": "0.56.1",
  "exists": true
}

Storage

{
  "path": "~/.local/share/cortexkit/aft",
  "exists": true,
  "accessible": true,
  "sizesByKey": {
    "index": 40878495,
    "semantic": 194057629,
    "backups": 0,
    "url_cache": 0,
    "onnxruntime": 66492548,
    "logs": 3448586
  }
}

ONNX Runtime

{
  "required": true,
  "systemPath": null,
  "systemVersion": null,
  "systemCompatible": null,
  "ignoredSystemPath": null,
  "ignoredSystemReason": null,
  "cachedPath": "~/.local/share/cortexkit/aft/onnxruntime/1.24.4",
  "cachedVersion": "1.24.4",
  "cachedCompatible": true,
  "platform": "linux-x64",
  "installHint": "AFT auto-downloads ONNX Runtime on supported Linux (glibc)",
  "requirement": ">=1.20"
}

Log file

~/.local/share/cortexkit/aft/logs/aft-plugin.log (3043 KB)

Binary cache

{
  "versions": [
    "v0.55.1",
    "v0.56.0",
    "v0.56.1"
  ],
  "activeVersion": "v0.56.1",
  "totalSize": 268846600,
  "path": "~/.cache/aft/bin"
}

LSP cache

{
  "npm": {
    "path": "~/.cache/aft/lsp-packages",
    "entries": [
      {
        "name": "@biomejs/biome",
        "path": "~/.cache/aft/lsp-packages/%40biomejs%2Fbiome",
        "size": 64421772
      },
      {
        "name": "pyright",
        "path": "~/.cache/aft/lsp-packages/pyright",
        "size": 19346292
      },
      {
        "name": "yaml-language-server",
        "path": "~/.cache/aft/lsp-packages/yaml-language-server",
        "size": 19212560
      },
      {
        "name": "bash-language-server",
        "path": "~/.cache/aft/lsp-packages/bash-language-server",
        "size": 14521656
      },
      {
        "name": "typescript-language-server",
        "path": "~/.cache/aft/lsp-packages/typescript-language-server",
        "size": 3342821
      },
      {
        "name": "latex-lsp/texlab",
        "path": "~/.cache/aft/lsp-packages/latex-lsp%2Ftexlab",
        "size": 80
      },
      {
        "name": "clangd/clangd",
        "path": "~/.cache/aft/lsp-packages/clangd%2Fclangd",
        "size": 79
      }
    ],
    "totalSize": 120845260
  },
  "github": {
    "path": "~/.cache/aft/lsp-binaries",
    "entries": [
      {
        "name": "texlab",
        "path": "~/.cache/aft/lsp-binaries/texlab",
        "size": 33664431
      },
      {
        "name": "clangd",
        "path": "~/.cache/aft/lsp-binaries/clangd",
        "size": 119
      }
    ],
    "totalSize": 33664550
  },
  "totalSize": 154509810
}

Recent errors (last 20, sanitized)

[2026-09-17T07:09:46.360Z] INFO [aft-plugin] [aft] 2026-09-17T07:09:46Z [aft] callgraph store refresh failed: sqlite error: database is locked
[2026-09-17T08:56:52.895Z] INFO [aft-plugin] [aft] 2026-09-17T08:56:52Z [aft] callgraph store refresh failed: sqlite error: database is locked

Recent AFT tool failures

tool_call: timed out after 60000ms ×22
status: timed out after 5000ms ×4
bridge killed after timeout ×1

Logs (last 200 lines per harness)

OpenCode log (~/.local/share/cortexkit/aft/logs/aft-plugin.log)

[2026-09-17T13:08:03.726Z] INFO [aft-plugin] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-17T13:08:03.728Z] INFO [aft-plugin] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-17T13:08:03.732Z] INFO [aft-plugin] Resolved binary from versioned cache: ~/.cache/aft/bin/v0.56.1/aft
[2026-09-17T13:08:03.733Z] INFO [aft-plugin] AFT storage migration skipped for opencode: no legacy data at ~/.local/share/opencode/storage/plugin/aft; using ~/.local/share/cortexkit/aft for fresh install
[2026-09-17T13:08:03.734Z] INFO [aft-plugin] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-17T13:08:03.775Z] INFO [aft-plugin] ONNX Runtime found at ~/.local/share/cortexkit/aft/onnxruntime/1.24.4 (TOFU verified)
[2026-09-17T13:08:03.839Z] INFO [aft-plugin] [lsp] auto-install: 3 npm + 0 github install(s) running in background
[2026-09-17T13:08:03.852Z] INFO [aft-plugin] RPC server listening on 127.0.0.1:37485
[2026-09-17T13:08:03.866Z] INFO [aft-plugin] hashline activation decision requested=false edit_slot_survives=false effective=false
[2026-09-17T13:08:03.866Z] INFO [aft-plugin] Workflow hints injected (5246 chars)
[2026-09-17T13:08:03.866Z] INFO [aft-plugin] ONNX Runtime ready at ~/.local/share/cortexkit/aft/onnxruntime/1.24.4; new bridges will load semantic backend.
[2026-09-17T13:08:04.460Z] INFO [aft-plugin] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-17T13:08:04.460Z] INFO [aft-plugin] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-17T13:08:04.466Z] INFO [aft-plugin] Resolved binary from versioned cache: ~/.cache/aft/bin/v0.56.1/aft
[2026-09-17T13:08:04.466Z] INFO [aft-plugin] AFT storage migration skipped for opencode: no legacy data at ~/.local/share/opencode/storage/plugin/aft; using ~/.local/share/cortexkit/aft for fresh install
[2026-09-17T13:08:04.467Z] INFO [aft-plugin] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-17T13:08:04.493Z] INFO [aft-plugin] ONNX Runtime found at ~/.local/share/cortexkit/aft/onnxruntime/1.24.4 (TOFU verified)
[2026-09-17T13:08:04.493Z] INFO [aft-plugin] [lsp] skipping auto-install (another instance ran one recently)
[2026-09-17T13:08:04.519Z] INFO [aft-plugin] RPC server listening on 127.0.0.1:42269
[2026-09-17T13:08:04.533Z] INFO [aft-plugin] hashline activation decision requested=false edit_slot_survives=false effective=false
[2026-09-17T13:08:04.533Z] INFO [aft-plugin] Workflow hints injected (5246 chars)
[2026-09-17T13:08:04.547Z] INFO [aft-plugin] ONNX Runtime ready at ~/.local/share/cortexkit/aft/onnxruntime/1.24.4; new bridges will load semantic backend.
[2026-09-17T13:08:04.548Z] INFO [aft-plugin] [lsp] lsp_paths_extra updated after auto-install: 6 dirs pushed to live bridges
[2026-09-17T13:08:04.767Z] INFO [aft-plugin] [lsp] lsp_paths_extra updated after auto-install: 6 dirs pushed to live bridges
[2026-09-17T13:08:08.884Z] INFO [aft-plugin] [auto-update-checker] Skipping check (another instance ran one recently)
[2026-09-17T13:08:11.116Z] INFO [aft-plugin] [auto-update-checker] Skipping check (another instance ran one recently)
[2026-09-17T13:08:34.668Z] INFO [aft-plugin] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-17T13:08:34.785Z] INFO [aft-plugin] [bash_wait_detach] no active wait found for session ses_06c2e8539ffesJs6k0FYaOLtGB (signaled 2 bridge(s))
[2026-09-17T13:08:49.742Z] INFO [aft-plugin] [aft] 2026-09-17T13:08:49Z [aft] perf tier2_callgraph_snapshot: source=callgraph_store files=168 exports=0 edges=2721 entry_points=0 ms=396
[2026-09-17T13:08:50.580Z] INFO [aft-plugin] [aft] 2026-09-17T13:08:50Z [aft] perf tier2 phases category=dead_code freshness=0ms snapshot=400ms projection_ms=108 scan=412ms(168 files) db=50ms(lock=0,txn=50) rollup_ms=291 rollup=full reason=cold projection=full reason=cold journal_bytes=0 changed_files=0 root=~/DEV/WEB/79mplus/arabic-lab-research-and-dev key=<REDACTED_SECRET>
[2026-09-17T13:08:50.580Z] INFO [aft-plugin] [aft] 2026-09-17T13:08:50Z [aft] perf tier2 category=dead_code reuse=miss ms=1407
[2026-09-17T13:08:50.580Z] INFO [aft-plugin] [aft] 2026-09-17T13:08:50Z [aft] index_event kind=build_started plane=tier2 build_id=b-1216275-4 root=~/DEV/WEB/79mplus/arabic-lab-research-and-dev key=<REDACTED_SECRET> category=dead_code files=168
[2026-09-17T13:08:50.580Z] INFO [aft-plugin] [aft] 2026-09-17T13:08:50Z [aft] index_event kind=build_ready plane=tier2 build_id=b-1216275-4 root=~/DEV/WEB/79mplus/arabic-lab-research-and-dev key=<REDACTED_SECRET> category=dead_code elapsed_ms=1407 files=168 contributions=168
[2026-09-17T13:08:51.188Z] INFO [aft-plugin] [aft] 2026-09-17T13:08:51Z [aft] perf tier2 phases category=unused_exports freshness=0ms snapshot=0ms projection_ms=0 scan=182ms(168 files) db=51ms(lock=0,txn=51) rollup_ms=176 projection=none reason=not_required journal_bytes=0 changed_files=0 root=~/DEV/WEB/79mplus/arabic-lab-research-and-dev key=<REDACTED_SECRET>
[2026-09-17T13:08:51.188Z] INFO [aft-plugin] [aft] 2026-09-17T13:08:51Z [aft] perf tier2 category=unused_exports reuse=miss ms=607
[2026-09-17T13:08:51.188Z] INFO [aft-plugin] [aft] 2026-09-17T13:08:51Z [aft] index_event kind=build_started plane=tier2 build_id=b-1216275-5 root=~/DEV/WEB/79mplus/arabic-lab-research-and-dev key=<REDACTED_SECRET> category=unused_exports files=168
[2026-09-17T13:08:51.188Z] INFO [aft-plugin] [aft] 2026-09-17T13:08:51Z [aft] index_event kind=build_ready plane=tier2 build_id=b-1216275-5 root=~/DEV/WEB/79mplus/arabic-lab-research-and-dev key=<REDACTED_SECRET> category=unused_exports elapsed_ms=607 files=168 contributions=168
[2026-09-17T13:08:51.412Z] INFO [aft-plugin] [aft] 2026-09-17T13:08:51Z [aft] perf tier2 phases category=duplicates freshness=0ms snapshot=0ms projection_ms=0 scan=23ms(168 files) db=26ms(lock=0,txn=26) rollup_ms=2 projection=none reason=not_required journal_bytes=0 changed_files=0 root=~/DEV/WEB/79mplus/arabic-lab-research-and-dev key=<REDACTED_SECRET>
[2026-09-17T13:08:51.413Z] INFO [aft-plugin] [aft] 2026-09-17T13:08:51Z [aft] perf tier2 category=duplicates reuse=miss ms=224
[2026-09-17T13:08:51.413Z] INFO [aft-plugin] [aft] 2026-09-17T13:08:51Z [aft] index_event kind=build_started plane=tier2 build_id=b-1216275-6 root=~/DEV/WEB/79mplus/arabic-lab-research-and-dev key=<REDACTED_SECRET> category=duplicates files=168
[2026-09-17T13:08:51.413Z] INFO [aft-plugin] [aft] 2026-09-17T13:08:51Z [aft] index_event kind=build_ready plane=tier2 build_id=b-1216275-6 root=~/DEV/WEB/79mplus/arabic-lab-research-and-dev key=<REDACTED_SECRET> category=duplicates elapsed_ms=224 files=168 contributions=168
[2026-09-17T13:08:51.709Z] INFO [aft-plugin] [aft] 2026-09-17T13:08:51Z [aft] perf tier2 phases category=cycles freshness=0ms snapshot=0ms projection_ms=0 scan=74ms(168 files) db=47ms(lock=0,txn=47) rollup_ms=0 projection=none reason=not_required journal_bytes=0 changed_files=0 root=~/DEV/WEB/79mplus/arabic-lab-research-and-dev key=<REDACTED_SECRET>
[2026-09-17T13:08:51.709Z] INFO [aft-plugin] [aft] 2026-09-17T13:08:51Z [aft] perf tier2 category=cycles reuse=miss ms=291
[2026-09-17T13:08:51.709Z] INFO [aft-plugin] [aft] 2026-09-17T13:08:51Z [aft] index_event kind=build_started plane=tier2 build_id=b-1216275-7 root=~/DEV/WEB/79mplus/arabic-lab-research-and-dev key=<REDACTED_SECRET> category=cycles files=168
[2026-09-17T13:08:51.709Z] INFO [aft-plugin] [aft] 2026-09-17T13:08:51Z [aft] index_event kind=build_ready plane=tier2 build_id=b-1216275-7 root=~/DEV/WEB/79mplus/arabic-lab-research-and-dev key=<REDACTED_SECRET> category=cycles elapsed_ms=291 files=168 contributions=168
[2026-09-17T13:08:51.952Z] INFO [aft-plugin] [aft] 2026-09-17T13:08:51Z [aft] perf tier2 phases category=complexity freshness=0ms snapshot=0ms projection_ms=0 scan=31ms(168 files) db=23ms(lock=0,txn=23) rollup_ms=21 projection=none reason=not_required journal_bytes=0 changed_files=0 root=~/DEV/WEB/79mplus/arabic-lab-research-and-dev key=<REDACTED_SECRET>
[2026-09-17T13:08:51.952Z] INFO [aft-plugin] [aft] 2026-09-17T13:08:51Z [aft] perf tier2 category=complexity reuse=miss ms=244
[2026-09-17T13:08:51.952Z] INFO [aft-plugin] [aft] 2026-09-17T13:08:51Z [aft] index_event kind=build_started plane=tier2 build_id=b-1216275-8 root=~/DEV/WEB/79mplus/arabic-lab-research-and-dev key=<REDACTED_SECRET> category=complexity files=168
[2026-09-17T13:08:51.952Z] INFO [aft-plugin] [aft] 2026-09-17T13:08:51Z [aft] index_event kind=build_ready plane=tier2 build_id=b-1216275-8 root=~/DEV/WEB/79mplus/arabic-lab-research-and-dev key=<REDACTED_SECRET> category=complexity elapsed_ms=244 files=168 contributions=168
[2026-09-17T13:09:34.387Z] INFO [aft-plugin] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-17T13:09:34.388Z] WARN [aft-plugin] [bash_wait_detach] no live bridge for session ses_f50a5ff64ffeNUAkYtA87ImyuE (root <PROJECT>)
[2026-09-17T13:10:18.523Z] WARN [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] [aft-plugin] bg-notifications: drain failed {"event":"bash_completion_drain_error","cause":"active bridge unavailable for <PROJECT>","canonical_root":"<PROJECT>","suppressed":0}
[2026-09-17T13:10:28.858Z] INFO [aft-plugin] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-17T13:10:28.858Z] WARN [aft-plugin] [bash_wait_detach] no live bridge for session ses_f50a5ff64ffeNUAkYtA87ImyuE (root <PROJECT>)
[2026-09-17T13:10:52.427Z] INFO [aft-plugin] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-17T13:10:52.427Z] WARN [aft-plugin] [bash_wait_detach] no live bridge for session ses_f50a5ff64ffeNUAkYtA87ImyuE (root <PROJECT>)
[2026-09-17T13:11:06.429Z] INFO [aft-plugin] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-17T13:11:06.430Z] INFO [aft-plugin] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-17T13:11:06.439Z] INFO [aft-plugin] Resolved binary from versioned cache: ~/.cache/aft/bin/v0.56.1/aft
[2026-09-17T13:11:06.440Z] INFO [aft-plugin] AFT storage migration skipped for opencode: no legacy data at ~/.local/share/opencode/storage/plugin/aft; using ~/.local/share/cortexkit/aft for fresh install
[2026-09-17T13:11:06.441Z] INFO [aft-plugin] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-17T13:11:06.477Z] INFO [aft-plugin] ONNX Runtime found at ~/.local/share/cortexkit/aft/onnxruntime/1.24.4 (TOFU verified)
[2026-09-17T13:11:06.530Z] INFO [aft-plugin] [lsp] auto-install: 3 npm + 0 github install(s) running in background
[2026-09-17T13:11:06.540Z] INFO [aft-plugin] RPC server listening on 127.0.0.1:38017
[2026-09-17T13:11:06.554Z] INFO [aft-plugin] hashline activation decision requested=false edit_slot_survives=false effective=false
[2026-09-17T13:11:06.555Z] INFO [aft-plugin] Workflow hints injected (5246 chars)
[2026-09-17T13:11:06.555Z] INFO [aft-plugin] ONNX Runtime ready at ~/.local/share/cortexkit/aft/onnxruntime/1.24.4; new bridges will load semantic backend.
[2026-09-17T13:11:07.103Z] INFO [aft-plugin] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-17T13:11:07.103Z] INFO [aft-plugin] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-17T13:11:07.109Z] INFO [aft-plugin] Resolved binary from versioned cache: ~/.cache/aft/bin/v0.56.1/aft
[2026-09-17T13:11:07.109Z] INFO [aft-plugin] AFT storage migration skipped for opencode: no legacy data at ~/.local/share/opencode/storage/plugin/aft; using ~/.local/share/cortexkit/aft for fresh install
[2026-09-17T13:11:07.110Z] INFO [aft-plugin] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-17T13:11:07.128Z] INFO [aft-plugin] ONNX Runtime found at ~/.local/share/cortexkit/aft/onnxruntime/1.24.4 (TOFU verified)
[2026-09-17T13:11:07.128Z] INFO [aft-plugin] [lsp] skipping auto-install (another instance ran one recently)
[2026-09-17T13:11:07.163Z] INFO [aft-plugin] RPC server listening on 127.0.0.1:42407
[2026-09-17T13:11:07.168Z] INFO [aft-plugin] hashline activation decision requested=false edit_slot_survives=false effective=false
[2026-09-17T13:11:07.168Z] INFO [aft-plugin] Workflow hints injected (5246 chars)
[2026-09-17T13:11:07.182Z] INFO [aft-plugin] ONNX Runtime ready at ~/.local/share/cortexkit/aft/onnxruntime/1.24.4; new bridges will load semantic backend.
[2026-09-17T13:11:07.183Z] INFO [aft-plugin] [lsp] lsp_paths_extra updated after auto-install: 6 dirs pushed to live bridges
[2026-09-17T13:11:07.002Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] [subagent-detect] cache miss, calling client.session.get(id=ses_f50a5ff64ffeNUAkYtA87ImyuE)
[2026-09-17T13:11:07.019Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] [subagent-detect] SDK returned session=present, parentID=undefined → isSubagent=false
[2026-09-17T13:11:07.024Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] Spawning binary: ~/.cache/aft/bin/v0.56.1/aft (cwd: <PROJECT>)
[2026-09-17T13:11:07.024Z] INFO [aft-plugin] bridge.spawnProcess: useFastembedBackend=true, parentORT=(unset), ortLibraryPath=~/.local/share/cortexkit/aft/onnxruntime/1.24.4/libonnxruntime.so
[2026-09-17T13:11:07.024Z] INFO [aft-plugin] ORT_DYLIB_PATH set from managed ONNX Runtime: ~/.local/share/cortexkit/aft/onnxruntime/1.24.4/libonnxruntime.so
[2026-09-17T13:11:07.167Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] hashline registration carrier transport=ndjson phase=configure edit_slot_survives=false
[2026-09-17T13:11:07.168Z] INFO [aft-plugin] [aft] 2026-09-17T13:11:07Z [aft] log retention sweep: removed_files=0 bytes_freed=0 recycled_pids=0
[2026-09-17T13:11:07.168Z] INFO [aft-plugin] [aft] 2026-09-17T13:11:07Z [aft] login-shell PATH probe: source=cache shell=/usr/bin/fish elapsed_ms=2
[2026-09-17T13:11:07.168Z] INFO [aft-plugin] [aft] 2026-09-17T13:11:07Z [aft] started, pid 1239742
[2026-09-17T13:11:07.200Z] INFO [aft-plugin] [aft] 2026-09-17T13:11:07Z [aft] [ses_f50a5ff64ffeNUAkYtA87ImyuE] project root set: <PROJECT>
[2026-09-17T13:11:07.215Z] INFO [aft-plugin] [aft] 2026-09-17T13:11:07Z [aft] [ses_f50a5ff64ffeNUAkYtA87ImyuE] configure maintenance yielded to 1 queued request(s)
[2026-09-17T13:11:07.262Z] INFO [aft-plugin] [aft] 2026-09-17T13:11:07Z [aft] [ses_f50a5ff64ffeNUAkYtA87ImyuE] gitignore matcher built: 77 pattern(s)
[2026-09-17T13:11:07.263Z] INFO [aft-plugin] Binary version: 0.56.1
[2026-09-17T13:11:07.276Z] INFO [aft-plugin] [aft] 2026-09-17T13:11:07Z [aft] watcher exclusions for <PROJECT> (8): [<PROJECT>/.git, <PROJECT>/.kilo/node_modules, <PROJECT>/.kilocode/node_modules, <PROJECT>/.opencode/node_modules, <PROJECT>/node_modules, <PROJECT>/.next, <PROJECT>/.cortexkit/magic-context, <PROJECT>/.planning]
[2026-09-17T13:11:07.293Z] INFO [aft-plugin] [aft] 2026-09-17T13:11:07Z [aft] search index orphan sweep root=~/.local/share/cortexkit/aft/index scanned=11 removed=0 skipped_derived=1 skipped_memo=4 skipped_fresh=6 skipped_live=0 skipped_locked=0 skipped_unreadable=0 budget_exhausted=false
[2026-09-17T13:11:07.293Z] INFO [aft-plugin] [aft] 2026-09-17T13:11:07Z [aft] transient search cache sweep root=/tmp scanned=0 removed=0 bytes=0 skipped_fresh=0 skipped_unreadable=0 budget_exhausted=false
[2026-09-17T13:11:07.305Z] INFO [aft-plugin] [aft] 2026-09-17T13:11:07Z [aft] watcher started: <PROJECT>
[2026-09-17T13:11:07.295Z] INFO [aft-plugin] [lsp] lsp_paths_extra updated after auto-install: 6 dirs pushed to live bridges
[2026-09-17T13:11:07.590Z] INFO [aft-plugin] [aft] 2026-09-17T13:11:07Z [aft] [ses_f50a5ff64ffeNUAkYtA87ImyuE] search index: refreshed 335 stale file(s) from disk cache
[2026-09-17T13:11:08.008Z] INFO [aft-plugin] [aft] 2026-09-17T13:11:08Z [aft] [ses_f50a5ff64ffeNUAkYtA87ImyuE] loaded symbol cache from disk: 1328 files
[2026-09-17T13:11:08.043Z] INFO [aft-plugin] [aft] 2026-09-17T13:11:08Z [aft] [ses_f50a5ff64ffeNUAkYtA87ImyuE] local embedder ready: model=all-MiniLM-L6-v2 intra_threads=8 token_type_ids=<REDACTED_SECRET>
[2026-09-17T13:11:08.171Z] INFO [aft-plugin] [aft] 2026-09-17T13:11:08Z [aft] [ses_f50a5ff64ffeNUAkYtA87ImyuE] loaded semantic index from disk: 3612 entries (5 delta segments)
[2026-09-17T13:11:08.233Z] INFO [aft-plugin] [aft] 2026-09-17T13:11:08Z [aft] [ses_f50a5ff64ffeNUAkYtA87ImyuE] semantic index: cached index is current (3612 entries)
[2026-09-17T13:11:08.422Z] INFO [aft-plugin] [aft] 2026-09-17T13:11:08Z [aft] [ses_f50a5ff64ffeNUAkYtA87ImyuE] pre-warmed symbol cache: 0 new, 1328 cached, 1328 files total
[2026-09-17T13:11:09.383Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] perf tool=bash total=2383ms pre=20ms bridge=2362ms post=1ms
[2026-09-17T13:11:09.395Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] [aft-plugin] bg-notifications: drain ok {"event":"bash_completion_drain_ok","count":0,"task_ids":[],"canonical_root":"<PROJECT>","suppressed":0}
[2026-09-17T13:11:11.555Z] INFO [aft-plugin] [auto-update-checker] Skipping check (another instance ran one recently)
[2026-09-17T13:11:12.168Z] INFO [aft-plugin] [auto-update-checker] Skipping check (another instance ran one recently)
[2026-09-17T13:11:45.815Z] INFO [aft-plugin] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-17T13:11:45.815Z] WARN [aft-plugin] [bash_wait_detach] no live bridge for session ses_f50816387ffelYpqoEnN6f3V7Y (root <PROJECT>)
[2026-09-17T13:11:51.064Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] perf tool=bash total=47ms pre=3ms bridge=43ms post=0ms
[2026-09-17T13:11:57.485Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] perf tool=bash_status total=14ms pre=0ms bridge=13ms post=0ms
[2026-09-17T13:12:07.241Z] INFO [aft-plugin] [aft] 2026-09-17T13:12:07Z [aft] [ses_f50a5ff64ffeNUAkYtA87ImyuE] perf tick: watcher={ingested:0,paths:0,dropped:0} drains=10 tier2=[none] semantic={collects:0,files:0,chunks:0,ms:0} callgraph_invalidations=0 executor_completed={interactive:0,maintenance:0} oldest_queued_ms={interactive:none,maintenance:none} toolcall={new:0,window:0,p50_total_ms:0,max_total_ms:0,p50_queue_ms:0,max_queue_ms:0} file_log_dropped=0
[2026-09-17T13:12:11.308Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] perf tool=bash_write total=6ms pre=0ms bridge=6ms post=0ms
[2026-09-17T13:12:11.310Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] [aft-plugin] bg-notifications: drain ok {"event":"bash_completion_drain_ok","count":0,"task_ids":[],"canonical_root":"<PROJECT>","suppressed":2}
[2026-09-17T13:12:31.394Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] perf tool=bash_status total=23ms pre=0ms bridge=23ms post=0ms
[2026-09-17T13:12:50.084Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] perf tool=bash_write total=5ms pre=0ms bridge=5ms post=0ms
[2026-09-17T13:13:07.342Z] INFO [aft-plugin] [aft] 2026-09-17T13:13:07Z [aft] [ses_f50a5ff64ffeNUAkYtA87ImyuE] perf tick: watcher={ingested:0,paths:0,dropped:0} drains=7 tier2=[none] semantic={collects:0,files:0,chunks:0,ms:0} callgraph_invalidations=0 executor_completed={interactive:0,maintenance:0} oldest_queued_ms={interactive:none,maintenance:none} toolcall={new:0,window:0,p50_total_ms:0,max_total_ms:0,p50_queue_ms:0,max_queue_ms:0} file_log_dropped=0
[2026-09-17T13:13:35.922Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] perf tool=bash_status total=20ms pre=0ms bridge=20ms post=0ms
[2026-09-17T13:13:35.924Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] [aft-plugin] bg-notifications: drain ok {"event":"bash_completion_drain_ok","count":0,"task_ids":[],"canonical_root":"<PROJECT>","suppressed":2}
[2026-09-17T13:14:07.437Z] INFO [aft-plugin] [aft] 2026-09-17T13:14:07Z [aft] [ses_f50a5ff64ffeNUAkYtA87ImyuE] perf tick: watcher={ingested:0,paths:0,dropped:0} drains=2 tier2=[none] semantic={collects:0,files:0,chunks:0,ms:0} callgraph_invalidations=0 executor_completed={interactive:0,maintenance:0} oldest_queued_ms={interactive:none,maintenance:none} toolcall={new:0,window:0,p50_total_ms:0,max_total_ms:0,p50_queue_ms:0,max_queue_ms:0} file_log_dropped=0
[2026-09-17T13:14:09.423Z] INFO [aft-plugin] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-17T13:14:09.424Z] WARN [aft-plugin] [bash_wait_detach] no live bridge for session ses_f50816387ffelYpqoEnN6f3V7Y (root <PROJECT>)
[2026-09-17T13:14:15.977Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] perf tool=bash_write total=6ms pre=0ms bridge=6ms post=0ms
[2026-09-17T13:14:31.141Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] perf tool=bash_kill total=2011ms pre=0ms bridge=2011ms post=0ms
[2026-09-17T13:14:35.817Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] perf tool=bash total=33ms pre=5ms bridge=28ms post=0ms
[2026-09-17T13:14:35.819Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] [aft-plugin] bg-notifications: drain ok {"event":"bash_completion_drain_ok","count":1,"task_ids":["bash-3071e170518703d0"],"canonical_root":"<PROJECT>","suppressed":0}
[2026-09-17T13:14:35.820Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] [aft-plugin] bg-notifications: in-turn append {"event":"bash_completion_in_turn_append","task_ids":["bash-3071e170518703d0"],"long_running_task_ids":[],"reminder_sha256":"b0e4a97e0acecca3","reminder_chars":102}
[2026-09-17T13:14:35.846Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] [aft-plugin] bg-notifications: ack ok {"event":"bash_completion_ack_ok","delivery_id":null,"task_id":"bash-3071e170518703d0","task_ids":["bash-3071e170518703d0"],"canonical_root":"<PROJECT>","suppressed":0}
[2026-09-17T13:14:56.781Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] perf tool=bash_status total=5ms pre=0ms bridge=5ms post=0ms
[2026-09-17T13:14:56.783Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] [aft-plugin] bg-notifications: drain ok {"event":"bash_completion_drain_ok","count":0,"task_ids":[],"canonical_root":"<PROJECT>","suppressed":2}
[2026-09-17T13:15:07.537Z] INFO [aft-plugin] [aft] 2026-09-17T13:15:07Z [aft] [ses_f50a5ff64ffeNUAkYtA87ImyuE] perf tick: watcher={ingested:0,paths:0,dropped:0} drains=10 tier2=[none] semantic={collects:0,files:0,chunks:0,ms:0} callgraph_invalidations=0 executor_completed={interactive:0,maintenance:0} oldest_queued_ms={interactive:none,maintenance:none} toolcall={new:0,window:0,p50_total_ms:0,max_total_ms:0,p50_queue_ms:0,max_queue_ms:0} file_log_dropped=0
[2026-09-17T13:15:09.075Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] perf tool=bash_write total=14ms pre=0ms bridge=14ms post=0ms
[2026-09-17T13:15:24.737Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] perf tool=bash_write total=6ms pre=0ms bridge=6ms post=0ms
[2026-09-17T13:15:49.303Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] perf tool=bash_status total=12ms pre=0ms bridge=12ms post=0ms
[2026-09-17T13:16:08.888Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] perf tool=bash_kill total=2023ms pre=0ms bridge=2023ms post=0ms
[2026-09-17T13:16:08.890Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] [aft-plugin] bg-notifications: drain ok {"event":"bash_completion_drain_ok","count":0,"task_ids":[],"canonical_root":"<PROJECT>","suppressed":3}
[2026-09-17T13:16:08.890Z] INFO [aft-plugin] [aft] 2026-09-17T13:16:08Z [aft] [ses_f50a5ff64ffeNUAkYtA87ImyuE] perf tick: watcher={ingested:0,paths:0,dropped:0} drains=7 tier2=[none] semantic={collects:0,files:0,chunks:0,ms:0} callgraph_invalidations=0 executor_completed={interactive:0,maintenance:0} oldest_queued_ms={interactive:none,maintenance:none} toolcall={new:0,window:0,p50_total_ms:0,max_total_ms:0,p50_queue_ms:0,max_queue_ms:0} file_log_dropped=0
[2026-09-17T13:16:44.705Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] perf tool=bash total=38ms pre=4ms bridge=34ms post=0ms
[2026-09-17T13:16:44.708Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] [aft-plugin] bg-notifications: drain ok {"event":"bash_completion_drain_ok","count":1,"task_ids":["bash-1e7d4ed6ab958128"],"canonical_root":"<PROJECT>","suppressed":0}
[2026-09-17T13:16:44.708Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] [aft-plugin] bg-notifications: in-turn append {"event":"bash_completion_in_turn_append","task_ids":["bash-1e7d4ed6ab958128"],"long_running_task_ids":[],"reminder_sha256":"626d818cce181434","reminder_chars":102}
[2026-09-17T13:16:44.712Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] [aft-plugin] bg-notifications: ack ok {"event":"bash_completion_ack_ok","delivery_id":null,"task_id":"bash-1e7d4ed6ab958128","task_ids":["bash-1e7d4ed6ab958128"],"canonical_root":"<PROJECT>","suppressed":0}
[2026-09-17T13:17:09.128Z] INFO [aft-plugin] [aft] 2026-09-17T13:17:09Z [aft] [ses_f50a5ff64ffeNUAkYtA87ImyuE] perf tick: watcher={ingested:0,paths:0,dropped:0} drains=7 tier2=[none] semantic={collects:0,files:0,chunks:0,ms:0} callgraph_invalidations=0 executor_completed={interactive:0,maintenance:0} oldest_queued_ms={interactive:none,maintenance:none} toolcall={new:0,window:0,p50_total_ms:0,max_total_ms:0,p50_queue_ms:0,max_queue_ms:0} file_log_dropped=0
[2026-09-17T13:18:29.655Z] INFO [aft-plugin] bridge.spawnProcess: useFastembedBackend=true, parentORT=(unset), ortLibraryPath=~/.local/share/cortexkit/aft/onnxruntime/1.24.4/libonnxruntime.so
[2026-09-17T13:18:29.655Z] INFO [aft-plugin] ORT_DYLIB_PATH set from managed ONNX Runtime: ~/.local/share/cortexkit/aft/onnxruntime/1.24.4/libonnxruntime.so
[2026-09-17T13:18:29.811Z] INFO [aft-plugin] [aft] 2026-09-17T13:18:29Z [aft] log retention sweep: removed_files=0 bytes_freed=0 recycled_pids=0
[2026-09-17T13:18:29.811Z] INFO [aft-plugin] [aft] 2026-09-17T13:18:29Z [aft] login-shell PATH probe: source=cache shell=/usr/bin/fish elapsed_ms=0
[2026-09-17T13:18:29.811Z] INFO [aft-plugin] [aft] 2026-09-17T13:18:29Z [aft] started, pid 1261691
[2026-09-17T13:18:29.890Z] INFO [aft-plugin] Binary version: 0.56.1
[2026-09-17T13:18:29.898Z] INFO [aft-plugin] [aft] 2026-09-17T13:18:29Z [aft] search index orphan sweep root=~/.local/share/cortexkit/aft/index scanned=11 removed=0 skipped_derived=1 skipped_memo=4 skipped_fresh=6 skipped_live=0 skipped_locked=0 skipped_unreadable=0 budget_exhausted=false
[2026-09-17T13:18:29.898Z] INFO [aft-plugin] [aft] 2026-09-17T13:18:29Z [aft] transient search cache sweep root=/tmp scanned=0 removed=0 bytes=0 skipped_fresh=0 skipped_unreadable=0 budget_exhausted=false
[2026-09-17T13:18:29.899Z] INFO [aft-plugin] [aft] 2026-09-17T13:18:29Z [aft] watcher exclusions for <PROJECT> (8): [<PROJECT>/.git, <PROJECT>/.kilo/node_modules, <PROJECT>/.kilocode/node_modules, <PROJECT>/.opencode/node_modules, <PROJECT>/node_modules, <PROJECT>/.next, <PROJECT>/.cortexkit/magic-context, <PROJECT>/.planning]
[2026-09-17T13:18:29.917Z] INFO [aft-plugin] [aft] 2026-09-17T13:18:29Z [aft] watcher started: <PROJECT>
[2026-09-17T13:18:29.928Z] INFO [aft-plugin] [aft] 2026-09-17T13:18:29Z [aft] removing filesystem lock at ~/.local/share/cortexkit/aft/inspect/8311df43943b5155/writer.lease from dead or recycled PID 1161892
[2026-09-17T13:18:30.007Z] INFO [aft-plugin] [aft] 2026-09-17T13:18:30Z [aft] index_event kind=build_started plane=tier2 build_id=b-1261691-1 root=<PROJECT> key=<REDACTED_SECRET> category=dead_code files=0
[2026-09-17T13:18:30.007Z] INFO [aft-plugin] [aft] 2026-09-17T13:18:30Z [aft] index_event kind=build_ready plane=tier2 build_id=b-1261691-1 root=<PROJECT> key=<REDACTED_SECRET> category=dead_code elapsed_ms=116 files=0 contributions=0
[2026-09-17T13:18:30.081Z] INFO [aft-plugin] [aft] 2026-09-17T13:18:30Z [aft] index_event kind=build_started plane=tier2 build_id=b-1261691-2 root=<PROJECT> key=<REDACTED_SECRET> category=unused_exports files=0
[2026-09-17T13:18:30.081Z] INFO [aft-plugin] [aft] 2026-09-17T13:18:30Z [aft] index_event kind=build_ready plane=tier2 build_id=b-1261691-2 root=<PROJECT> key=<REDACTED_SECRET> category=unused_exports elapsed_ms=73 files=0 contributions=0
[2026-09-17T13:18:30.203Z] INFO [aft-plugin] [aft] 2026-09-17T13:18:30Z [aft] index_event kind=build_started plane=tier2 build_id=b-1261691-4 root=<PROJECT> key=<REDACTED_SECRET> category=cycles files=0
[2026-09-17T13:18:30.203Z] INFO [aft-plugin] [aft] 2026-09-17T13:18:30Z [aft] index_event kind=build_ready plane=tier2 build_id=b-1261691-4 root=<PROJECT> key=<REDACTED_SECRET> category=cycles elapsed_ms=73 files=0 contributions=0
[2026-09-17T13:18:31.711Z] INFO [aft-plugin] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-17T13:18:31.844Z] INFO [aft-plugin] [bash_wait_detach] no active wait found for session ses_f50a5ff64ffeNUAkYtA87ImyuE (signaled 2 bridge(s))
[2026-09-17T13:18:31.787Z] INFO [aft-plugin] [aft] 2026-09-17T13:18:31Z [aft] [ses_f50a5ff64ffeNUAkYtA87ImyuE] bash_wait_detach: session=ses_f50a5ff64ffeNUAkYtA87ImyuE detached=false active_wait_sessions=0
[2026-09-17T13:18:31.844Z] INFO [aft-plugin] [aft] 2026-09-17T13:18:31Z [aft] [ses_f50a5ff64ffeNUAkYtA87ImyuE] bash_wait_detach: session=ses_f50a5ff64ffeNUAkYtA87ImyuE detached=false active_wait_sessions=0
[2026-09-17T13:18:36.996Z] INFO [aft-plugin] [ses_f50a5ff64ffeNUAkYtA87ImyuE] [aft-plugin] bg-notifications: drain ok {"event":"bash_completion_drain_ok","count":0,"task_ids":[],"canonical_root":"<PROJECT>","suppressed":2}

Usernames and home paths have been stripped from this report.

Thanks for the full report. Two things are happening, and the second one is the one you see.

The 60 s timeout on the first multi-word query is under investigation (a 2K-file / 20 MB index with the local MiniLM backend should answer in well under a second on this shape; I am measuring where the time goes on Linux with the standalone bridge).

The search_engine_failed - re-verification of live memo entry at epoch 0 is rejected on the retry is a defect I can confirm from source: the exact-match memo marks a query's epoch as verified before the verification runs, so when the first attempt is abandoned by the timeout, the retry of the same query is refused instead of re-run. Single-word queries take a different lane, which is why they are unaffected. The fix makes an abandoned or in-flight verification retryable; it will ship in 0.56.2 alongside whatever the latency measurement finds.

In the meantime, changing the query wording (any different token set) gets a fresh memo key and will run.

Update. The retry refusal is fixed on main: exact-match verification is now single-flight per query, a second request for the same query joins the in-flight one instead of being refused, and a verification that is abandoned (timeout, cancel) or fails leaves the query retryable. That ships in 0.56.2.

On the 60 s first query: I could not reproduce it on a corpus of your shape (2,000 files / 24 MB index / 4,000 MiniLM entries) — cold first multi-word query 2.4 s, warm 1.6 s. Measuring did turn up one real cost on that path (every candidate file was scanned for multi-line phrase windows even when a query token was absent), which the same release cuts to 0.33 s warm. Whether that is your whole 60 s I cannot tell from here. Three things would settle it:

The exact query text that timed out (paste it verbatim; multi-word wording matters here).
The lines from ~/.local/share/cortexkit/aft/logs/aft-plugin.log in the minute around the timeout that contain perf tool=aft_search, deferred, or search — the phase timings are in them.
Whether the project directory is on a local disk or a network/overlay filesystem, and roughly how many files are in the repository.

If you are able to install a prerelease when 0.56.2 is tagged, retrying the same query on it would be the direct check.

I think this will help

That helps a lot — the screenshots split it cleanly. Every query that times out is natural-language shaped (where is the Remix panel mounted and option switching handled…, Remix panel mount option switch design page wiring), including the path-scoped one; the one that answers in 0.7 s (DesignOptionsSelector) is identifier-shaped. Identifier queries never embed; natural-language queries embed the query text with the local MiniLM model first. Path scoping shrinks the corpus scan but not the embed, so the shared cost that survives scoping is the embed, and reading our code I can confirm the query-time budget (3 s, then lexical fallback) is applied to HTTP embedding backends but not to the local ONNX one — if that call is slow on your machine, nothing bounds it and the whole search waits on it. That is a defect on our side regardless of why ONNX is slow there.

Two things to confirm it from your side:

In ~/.config/cortexkit/aft.jsonc, set "semantic_search": false temporarily, run the same natural-language query, and note whether it returns in under a few seconds (lexical only). Then set it back.
nproc and whether this is a VM/container with a CPU quota (ONNX Runtime spins worker threads sized to the visible core count; under a CPU quota that can turn a 20 ms inference into tens of seconds).

The fix in 0.56.2: the local embed runs under the same 3 s budget as the remote backends, a query that exceeds it falls back to lexical search with a visible note, and the embed duration is logged per query so this is never invisible again.

Released in v0.56.2 (npx @cortexkit/aft@latest setup, or update the plugin package to 0.56.2).

Both halves are in: the exact-match memo no longer rejects a retry after a timeout (verification is single-flight, and an abandoned attempt leaves the query retryable), and natural-language queries no longer stall on a slow local embedding — the bundled ONNX embed now runs under the same query budget as remote backends (3 s, then lexical results with a note), with ONNX threads capped by the container's CPU quota. Multi-word exact matching also skips files that cannot contain the phrase, which is what made the warm path slow in the first place.

If you still see a timeout on 0.56.2, npx @cortexkit/aft@latest doctor --issue would give me the timing lines to look at.

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AFT issue: After upgrading AFT from 0.56.0 to 0.56.1, semantic search times out on #319

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AFT issue: After upgrading AFT from 0.56.0 to 0.56.1, semantic search times out on #319

Description

Description

Environment

Diagnostics

OpenCode

Config paths

AFT flags

Plugin cache

Storage

ONNX Runtime

Log file

Binary cache

LSP cache

Recent errors (last 20, sanitized)

Recent AFT tool failures

Logs (last 200 lines per harness)

OpenCode log (~/.local/share/cortexkit/aft/logs/aft-plugin.log)

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aft-alfonso commented on Sep 17, 2026

aft-alfonso commented on Sep 17, 2026

Tahmid-kabir-addin commented on Sep 17, 2026

aft-alfonso commented on Sep 17, 2026

aft-alfonso commented on Sep 17, 2026

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