AFT issue: </system-reminder>```. Closing and reopening pi repeats it.

[aredridel]

Description

I closed pi; ran pi update --all; opened pi, got this:

 <system-reminder>
 [BG BASH NOTIFY]
 - task bash-e3d611742251a573 exited:
       > watch target erased: the background task row was erased before the watch reached a normal terminal result
 </system-reminder>

. Closing and reopening pi repeats it.

Environment

• AFT CLI: v0.55.1
• AFT binary: 0.55.1
• OS: linux x64
• Node: v26.7.0
• Session: ses_01a08199-aa74-766e-8c1d-0be5e7b2aca3 ( [BG BASH NOTIFY] - task bash-e3d611742251…)

Diagnostics

• Timestamp: 2026-09-08T15:27:13.053Z
• AFT CLI: v0.55.1
• AFT binary: 0.55.1
• OS: linux x64
• Node: v26.7.0

Pi

• Host installed: true
• Host version: 0.85.1
• Plugin registered: true
• Plugin version: 0.55.1
• AFT enabled: true
• AFT config parse error: none

Config paths

{
  "configDir": "~/.pi/agent",
  "harnessConfig": "~/.pi/agent/settings.json",
  "harnessConfigFormat": "json",
  "aftConfig": "~/.config/cortexkit/aft.jsonc",
  "aftConfigFormat": "jsonc"
}

AFT flags

{
  "bash": {
    "rewrite": true,
    "background": true
  },
  "semantic_search": true,
  "search_index": true,
  "tool_surface": "all",
  "$schema": "https://raw.githubusercontent.com/cortexkit/aft/master/assets/aft.schema.json"
}

Plugin cache

{
  "path": "~/.pi/agent/npm/node_modules/@cortexkit/aft-pi/package.json",
  "cached": "0.55.1",
  "exists": true
}

Storage

{
  "path": "~/.local/share/cortexkit/aft",
  "exists": true,
  "accessible": true,
  "sizesByKey": {
    "index": 97504691,
    "semantic": 1070819410,
    "backups": 0,
    "url_cache": 0,
    "onnxruntime": 66492548,
    "logs": 16861069
  },
  "legacyDuplication": {
    "totalPartitions": 48,
    "totalBytes": 572234686,
    "byHarness": [
      {
        "harness": "opencode",
        "partitions": 14,
        "bytes": 167507762
      },
      {
        "harness": "pi",
        "partitions": 34,
        "bytes": 404726924
      }
    ]
  }
}

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 (16267 KB)

Binary cache

{
  "versions": [
    "v0.16.1",
    "v0.35.1",
    "v0.35.4",
    "v0.36.1",
    "v0.37.0",
    "v0.37.1",
    "v0.37.2",
    "v0.39.4",
    "v0.40.1",
    "v0.40.2",
    "v0.40.3",
    "v0.41.0",
    "v0.42.0",
    "v0.43.0",
    "v0.45.1",
    "v0.46.0",
    "v0.47.0",
    "v0.47.1",
    "v0.47.2",
    "v0.47.3",
    "v0.48.0",
    "v0.48.1",
    "v0.49.0",
    "v0.49.1",
    "v0.49.2",
    "v0.49.3",
    "v0.49.4",
    "v0.51.1",
    "v0.51.2",
    "v0.51.3",
    "v0.52.1",
    "v0.52.2",
    "v0.53.0",
    "v0.54.0",
    "v0.55.0",
    "v0.55.1"
  ],
  "activeVersion": "v0.55.1",
  "totalSize": 2647241928,
  "path": "~/.cache/aft/bin"
}

LSP cache

{
  "npm": {
    "path": "~/.cache/aft/lsp-packages",
    "entries": [
      {
        "name": "@biomejs/biome",
        "path": "~/.cache/aft/lsp-packages/%40biomejs%2Fbiome",
        "size": 69080318
      },
      {
        "name": "@astrojs/language-server",
        "path": "~/.cache/aft/lsp-packages/%40astrojs%2Flanguage-server",
        "size": 61337948
      },
      {
        "name": "svelte-language-server",
        "path": "~/.cache/aft/lsp-packages/svelte-language-server",
        "size": 52064005
      },
      {
        "name": "pyright",
        "path": "~/.cache/aft/lsp-packages/pyright",
        "size": 19346292
      },
      {
        "name": "yaml-language-server",
        "path": "~/.cache/aft/lsp-packages/yaml-language-server",
        "size": 17794933
      },
      {
        "name": "bash-language-server",
        "path": "~/.cache/aft/lsp-packages/bash-language-server",
        "size": 14513389
      },
      {
        "name": "typescript-language-server",
        "path": "~/.cache/aft/lsp-packages/typescript-language-server",
        "size": 3342821
      },
      {
        "name": "dockerfile-language-server-nodejs",
        "path": "~/.cache/aft/lsp-packages/dockerfile-language-server-nodejs",
        "size": 2464530
      },
      {
        "name": "LuaLS/lua-language-server",
        "path": "~/.cache/aft/lsp-packages/LuaLS%2Flua-language-server",
        "size": 79
      },
      {
        "name": "clangd/clangd",
        "path": "~/.cache/aft/lsp-packages/clangd%2Fclangd",
        "size": 79
      }
    ],
    "totalSize": 239944394
  },
  "github": {
    "path": "~/.cache/aft/lsp-binaries",
    "entries": [
      {
        "name": "clangd",
        "path": "~/.cache/aft/lsp-binaries/clangd",
        "size": 373473970
      },
      {
        "name": "lua-ls",
        "path": "~/.cache/aft/lsp-binaries/lua-ls",
        "size": 21034721
      }
    ],
    "totalSize": 394508691
  },
  "totalSize": 634453085
}

Recent errors (last 20, sanitized)

[2026-09-03T18:22:49.490Z] INFO [aft-pi] [aft] 2026-09-03T18:22:49Z [aft] callgraph store refresh failed: sqlite error: database is locked
[2026-09-03T19:43:54.605Z] INFO [aft-pi] [aft] 2026-09-03T19:43:54Z [aft] callgraph store refresh failed: sqlite error: database is locked
[2026-09-03T22:02:16.006Z] WARN [aft-pi] Version check failed: [aft-pi] Bridge shutting down
[2026-09-03T22:02:16.007Z] WARN [aft-pi] [lsp] live bridge lsp_paths_extra update failed: Error: [aft-pi] Bridge shutting down
[2026-09-03T22:02:16.007Z] INFO [aft-pi] eager configure failed: [aft-pi] Bridge shutting down

Recent AFT tool failures

• bash: timed out after 25000ms ×1

Logs (last 200 lines per harness)

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

[2026-09-08T14:51:10.054Z] INFO [aft-pi] [lsp] auto-install: 1 npm + 0 github install(s) running in background
[2026-09-08T14:51:10.057Z] INFO [aft-pi] 🔧 AFT: ✨ v0.54.0:
  • Callgraph stays consistent under load: edits arriving mid-rebuild can no longer be silently lost from navigation results.
  • aft_zoom handles real-world .jsonc: files with comment banners above the opening brace now resolve, and not-found errors point at the segment that actually failed (thanks @iceteaSA).
  • Disk hygiene: stale per-checkout inspect caches from old worktrees are now swept automatically — one machine reclaimed 21 GB.

Join us on Discord: https://discord.gg/DSa65w8wuf
[2026-09-08T14:51:10.061Z] INFO [aft-pi] Workflow hints injected (5064 chars)
[2026-09-08T14:51:10.061Z] INFO [aft-pi] AFT extension ready (surface=all)
[2026-09-08T14:51:10.061Z] INFO [aft-pi] ONNX Runtime ready at ~/.local/share/cortexkit/aft/onnxruntime/1.24.4; new bridges will load semantic backend.
[2026-09-08T14:51:10.062Z] INFO [aft-pi] Spawning binary: ~/.cache/aft/bin/v0.54.0/aft (cwd: ~/Projects/github.com/spice-labs-inc/basil)
[2026-09-08T14:51:10.062Z] INFO [aft-pi] bridge.spawnProcess: useFastembedBackend=true, parentORT=(unset), ortLibraryPath=~/.local/share/cortexkit/aft/onnxruntime/1.24.4/libonnxruntime.so
[2026-09-08T14:51:10.062Z] INFO [aft-pi] ORT_DYLIB_PATH set from managed ONNX Runtime: ~/.local/share/cortexkit/aft/onnxruntime/1.24.4/libonnxruntime.so
[2026-09-08T14:51:10.918Z] INFO [aft-pi] hashline registration carrier transport=ndjson phase=configure edit_slot_survives=false
[2026-09-08T14:51:11.081Z] INFO [aft-pi] [aft] 2026-09-08T14:51:10Z [aft] log retention sweep: removed_files=0 bytes_freed=0
[2026-09-08T14:51:11.081Z] INFO [aft-pi] [aft] 2026-09-08T14:51:10Z [aft] started, pid 641067
[2026-09-08T14:51:11.081Z] INFO [aft-pi] [aft] 2026-09-08T14:51:10Z [aft] project root set: ~/Projects/github.com/spice-labs-inc/basil
[2026-09-08T14:51:11.081Z] INFO [aft-pi] [aft] 2026-09-08T14:51:10Z [aft] gitignore matcher built: 7 pattern(s)
[2026-09-08T14:51:11.081Z] INFO [aft-pi] [aft] 2026-09-08T14:51:10Z [aft] search index orphan sweep root=~/.local/share/cortexkit/aft/index scanned=31 removed=0 skipped_derived=1 skipped_memo=29 skipped_fresh=1 skipped_live=0 skipped_locked=0 skipped_unreadable=0 budget_exhausted=false
[2026-09-08T14:51:11.081Z] INFO [aft-pi] [aft] 2026-09-08T14:51:11Z [aft] quarantining unresolved background task bash-84319d597c5c02c2: background task layout not found
[2026-09-08T14:51:11.081Z] INFO [aft-pi] [aft] 2026-09-08T14:51:11Z [aft] loaded symbol cache from disk: 38 files
[2026-09-08T14:51:11.081Z] INFO [aft-pi] [aft] 2026-09-08T14:51:11Z [aft] pre-warmed symbol cache: 0 new, 38 cached, 38 files total
[2026-09-08T14:51:11.081Z] INFO [aft-pi] [aft] 2026-09-08T14:51:11Z [aft] callgraph store warm deferred until semantic cold seed gate clears or completes
[2026-09-08T14:51:11.081Z] INFO [aft-pi] [aft] 2026-09-08T14:51:11Z [aft] cannot establish filesystem boundary for checkpoint sweep ~/.local/share/cortexkit/aft/pi/checkpoints
[2026-09-08T14:51:11.208Z] INFO [aft-pi] Binary version: 0.54.0
[2026-09-08T14:53:34.068Z] INFO [aft-pi] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-08T14:53:34.070Z] INFO [aft-pi] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-08T14:53:34.070Z] INFO [aft-pi] AFT extension loading (plugin v0.55.1)
[2026-09-08T14:53:34.128Z] INFO [aft-pi] Copied npm binary to versioned cache: ~/.cache/aft/bin/v0.55.1/aft
[2026-09-08T14:53:34.128Z] INFO [aft-pi] Resolved binary from npm platform package: ~/.cache/aft/bin/v0.55.1/aft
[2026-09-08T14:53:34.129Z] INFO [aft-pi] AFT storage already migrated for pi; using ~/.local/share/cortexkit/aft
[2026-09-08T14:53:34.227Z] INFO [aft-pi] ONNX Runtime found at ~/.local/share/cortexkit/aft/onnxruntime/1.24.4 (TOFU verified)
[2026-09-08T14:53:34.228Z] INFO [aft-pi] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-08T14:53:34.861Z] INFO [aft-pi] [lsp] auto-install: 1 npm + 0 github install(s) running in background
[2026-09-08T14:53:34.864Z] INFO [aft-pi] 🔧 AFT: ✨ v0.55.1:
  • Callgraph stays consistent under load: edits arriving mid-rebuild can no longer be silently lost from navigation results.
  • aft_zoom handles real-world .jsonc: files with comment banners above the opening brace now resolve, and not-found errors point at the segment that actually failed (thanks @iceteaSA).
  • Disk hygiene: stale per-checkout inspect caches from old worktrees are now swept automatically — one machine reclaimed 21 GB.

Join us on Discord: https://discord.gg/DSa65w8wuf
[2026-09-08T14:53:34.866Z] INFO [aft-pi] Workflow hints injected (5064 chars)
[2026-09-08T14:53:34.867Z] INFO [aft-pi] AFT extension ready (surface=all)
[2026-09-08T14:53:34.867Z] INFO [aft-pi] ONNX Runtime ready at ~/.local/share/cortexkit/aft/onnxruntime/1.24.4; new bridges will load semantic backend.
[2026-09-08T14:53:34.869Z] INFO [aft-pi] Spawning binary: ~/.cache/aft/bin/v0.55.1/aft (cwd: ~/Projects/github.com/spice-labs-inc/basil)
[2026-09-08T14:53:34.869Z] INFO [aft-pi] bridge.spawnProcess: useFastembedBackend=true, parentORT=(unset), ortLibraryPath=~/.local/share/cortexkit/aft/onnxruntime/1.24.4/libonnxruntime.so
[2026-09-08T14:53:34.869Z] INFO [aft-pi] ORT_DYLIB_PATH set from managed ONNX Runtime: ~/.local/share/cortexkit/aft/onnxruntime/1.24.4/libonnxruntime.so
[2026-09-08T14:53:35.262Z] INFO [aft-pi] hashline registration carrier transport=ndjson phase=configure edit_slot_survives=false
[2026-09-08T14:53:36.571Z] INFO [aft-pi] [aft] 2026-09-08T14:53:35Z [aft] log retention sweep: removed_files=0 bytes_freed=0
[2026-09-08T14:53:36.571Z] INFO [aft-pi] [aft] 2026-09-08T14:53:35Z [aft] started, pid 647098
[2026-09-08T14:53:36.571Z] INFO [aft-pi] [aft] 2026-09-08T14:53:35Z [aft] project root set: ~/Projects/github.com/spice-labs-inc/basil
[2026-09-08T14:53:36.571Z] INFO [aft-pi] [aft] 2026-09-08T14:53:35Z [aft] gitignore matcher built: 7 pattern(s)
[2026-09-08T14:53:36.571Z] INFO [aft-pi] [aft] 2026-09-08T14:53:35Z [aft] search index orphan sweep root=~/.local/share/cortexkit/aft/index scanned=31 removed=0 skipped_derived=1 skipped_memo=29 skipped_fresh=1 skipped_live=0 skipped_locked=0 skipped_unreadable=0 budget_exhausted=false
[2026-09-08T14:53:36.571Z] INFO [aft-pi] [aft] 2026-09-08T14:53:35Z [aft] transient search cache sweep root=/tmp scanned=0 removed=0 bytes=0 skipped_fresh=0 skipped_unreadable=0 budget_exhausted=false
[2026-09-08T14:53:36.571Z] INFO [aft-pi] [aft] 2026-09-08T14:53:35Z [aft] quarantining unresolved background task bash-84319d597c5c02c2: background task layout not found
[2026-09-08T14:53:36.571Z] INFO [aft-pi] [aft] 2026-09-08T14:53:35Z [aft] loaded symbol cache from disk: 38 files
[2026-09-08T14:53:36.571Z] INFO [aft-pi] [aft] 2026-09-08T14:53:35Z [aft] pre-warmed symbol cache: 0 new, 38 cached, 38 files total
[2026-09-08T14:53:36.571Z] INFO [aft-pi] [aft] 2026-09-08T14:53:35Z [aft] callgraph store warm deferred until semantic cold seed gate clears or completes
[2026-09-08T14:53:36.571Z] INFO [aft-pi] [aft] 2026-09-08T14:53:35Z [aft] cannot establish filesystem boundary for checkpoint sweep ~/.local/share/cortexkit/aft/pi/checkpoints
[2026-09-08T14:53:36.571Z] INFO [aft-pi] [aft] 2026-09-08T14:53:35Z [aft] watcher started: ~/Projects/github.com/spice-labs-inc/basil
[2026-09-08T14:53:36.571Z] INFO [aft-pi] [aft] 2026-09-08T14:53:35Z [aft] local embedder ready: model=all-MiniLM-L6-v2 intra_threads=36 token_type_ids=<REDACTED_SECRET>
[2026-09-08T14:53:36.571Z] INFO [aft-pi] [aft] 2026-09-08T14:53:35Z [aft] loaded semantic index from disk: 351 entries
[2026-09-08T14:53:36.571Z] INFO [aft-pi] [aft] 2026-09-08T14:53:35Z [aft] semantic index: cached index is current (351 entries)
[2026-09-08T14:53:36.572Z] INFO [aft-pi] Binary version: 0.55.1
[2026-09-08T14:53:37.126Z] INFO [aft-pi] [aft] 2026-09-08T14:53:37Z [aft] project root set: ~/Projects/github.com/spice-labs-inc/basil
[2026-09-08T14:53:37.127Z] INFO [aft-pi] [lsp] lsp_paths_extra updated after auto-install: 10 dirs pushed to live bridges
[2026-09-08T14:53:37.130Z] INFO [aft-pi] [aft] 2026-09-08T14:53:37Z [aft] gitignore matcher built: 7 pattern(s)
[2026-09-08T14:53:37.130Z] INFO [aft-pi] [aft] 2026-09-08T14:53:37Z [aft] search index orphan sweep root=~/.local/share/cortexkit/aft/index scanned=31 removed=0 skipped_derived=1 skipped_memo=29 skipped_fresh=1 skipped_live=0 skipped_locked=0 skipped_unreadable=0 budget_exhausted=false
[2026-09-08T14:53:37.132Z] INFO [aft-pi] [aft] 2026-09-08T14:53:37Z [aft] transient search cache sweep root=/tmp scanned=0 removed=0 bytes=0 skipped_fresh=0 skipped_unreadable=0 budget_exhausted=false
[2026-09-08T14:53:37.142Z] INFO [aft-pi] [aft] 2026-09-08T14:53:37Z [aft] watcher stopped: ~/Projects/github.com/spice-labs-inc/basil
[2026-09-08T14:53:37.450Z] INFO [aft-pi] [aft] 2026-09-08T14:53:37Z [aft] watcher started: ~/Projects/github.com/spice-labs-inc/basil
[2026-09-08T14:53:48.111Z] INFO [aft-pi] Bridge pool shut down
[2026-09-08T14:53:56.489Z] INFO [aft-pi] Bridge pool shut down
[2026-09-08T15:17:50.032Z] INFO [aft-pi] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-08T15:17:50.034Z] INFO [aft-pi] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-08T15:17:50.034Z] INFO [aft-pi] AFT extension loading (plugin v0.55.1)
[2026-09-08T15:17:50.054Z] INFO [aft-pi] Resolved binary from versioned cache: ~/.cache/aft/bin/v0.55.1/aft
[2026-09-08T15:17:50.055Z] INFO [aft-pi] AFT storage already migrated for pi; using ~/.local/share/cortexkit/aft
[2026-09-08T15:17:50.155Z] INFO [aft-pi] ONNX Runtime found at ~/.local/share/cortexkit/aft/onnxruntime/1.24.4 (TOFU verified)
[2026-09-08T15:17:50.157Z] INFO [aft-pi] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-08T15:17:50.671Z] INFO [aft-pi] [lsp] auto-install: 2 npm + 0 github install(s) running in background
[2026-09-08T15:17:50.685Z] INFO [aft-pi] Workflow hints injected (5064 chars)
[2026-09-08T15:17:50.685Z] INFO [aft-pi] AFT extension ready (surface=all)
[2026-09-08T15:17:50.685Z] INFO [aft-pi] ONNX Runtime ready at ~/.local/share/cortexkit/aft/onnxruntime/1.24.4; new bridges will load semantic backend.
[2026-09-08T15:17:50.687Z] INFO [aft-pi] Spawning binary: ~/.cache/aft/bin/v0.55.1/aft (cwd: ~/Projects/github.com/spice-labs-inc/app-gitops)
[2026-09-08T15:17:50.687Z] INFO [aft-pi] bridge.spawnProcess: useFastembedBackend=true, parentORT=(unset), ortLibraryPath=~/.local/share/cortexkit/aft/onnxruntime/1.24.4/libonnxruntime.so
[2026-09-08T15:17:50.687Z] INFO [aft-pi] ORT_DYLIB_PATH set from managed ONNX Runtime: ~/.local/share/cortexkit/aft/onnxruntime/1.24.4/libonnxruntime.so
[2026-09-08T15:17:51.054Z] INFO [aft-pi] hashline registration carrier transport=ndjson phase=configure edit_slot_survives=false
[2026-09-08T15:17:51.499Z] INFO [aft-pi] [aft] 2026-09-08T15:17:50Z [aft] log retention sweep: removed_files=0 bytes_freed=0
[2026-09-08T15:17:51.499Z] INFO [aft-pi] [aft] 2026-09-08T15:17:50Z [aft] started, pid 704932
[2026-09-08T15:17:51.499Z] INFO [aft-pi] [aft] 2026-09-08T15:17:51Z [aft] project root set: ~/Projects/github.com/spice-labs-inc/app-gitops
[2026-09-08T15:17:51.499Z] INFO [aft-pi] [aft] 2026-09-08T15:17:51Z [aft] gitignore matcher built: 6 pattern(s)
[2026-09-08T15:17:51.499Z] INFO [aft-pi] [aft] 2026-09-08T15:17:51Z [aft] search index orphan sweep root=~/.local/share/cortexkit/aft/index scanned=31 removed=0 skipped_derived=1 skipped_memo=29 skipped_fresh=1 skipped_live=0 skipped_locked=0 skipped_unreadable=0 budget_exhausted=false
[2026-09-08T15:17:51.499Z] INFO [aft-pi] [aft] 2026-09-08T15:17:51Z [aft] transient search cache sweep root=/tmp scanned=0 removed=0 bytes=0 skipped_fresh=0 skipped_unreadable=0 budget_exhausted=false
[2026-09-08T15:17:51.499Z] INFO [aft-pi] [aft] 2026-09-08T15:17:51Z [aft] watcher started: ~/Projects/github.com/spice-labs-inc/app-gitops
[2026-09-08T15:17:51.499Z] INFO [aft-pi] [aft] 2026-09-08T15:17:51Z [aft] callgraph store warm deferred until semantic cold seed gate clears or completes
[2026-09-08T15:17:51.499Z] INFO [aft-pi] [aft] 2026-09-08T15:17:51Z [aft] cannot establish filesystem boundary for checkpoint sweep ~/.local/share/cortexkit/aft/pi/checkpoints
[2026-09-08T15:17:51.499Z] INFO [aft-pi] [aft] 2026-09-08T15:17:51Z [aft] loaded symbol cache from disk: 248 files
[2026-09-08T15:17:51.499Z] INFO [aft-pi] [aft] 2026-09-08T15:17:51Z [aft] pre-warmed symbol cache: 0 new, 248 cached, 248 files total
[2026-09-08T15:17:51.499Z] INFO [aft-pi] Binary version: 0.55.1
[2026-09-08T15:17:52.042Z] INFO [aft-pi] [aft] 2026-09-08T15:17:51Z [aft] local embedder ready: model=all-MiniLM-L6-v2 intra_threads=36 token_type_ids=<REDACTED_SECRET>
[2026-09-08T15:17:52.042Z] INFO [aft-pi] [aft] 2026-09-08T15:17:51Z [aft] loaded semantic index from disk: 602 entries
[2026-09-08T15:17:52.042Z] INFO [aft-pi] [aft] 2026-09-08T15:17:51Z [aft] semantic index: cached index is current (602 entries)
[2026-09-08T15:17:52.062Z] INFO [aft-pi] [aft] 2026-09-08T15:17:52Z [aft] project root set: ~/Projects/github.com/spice-labs-inc/app-gitops
[2026-09-08T15:17:52.063Z] INFO [aft-pi] [lsp] lsp_paths_extra updated after auto-install: 10 dirs pushed to live bridges
[2026-09-08T15:17:52.076Z] INFO [aft-pi] [aft] 2026-09-08T15:17:52Z [aft] gitignore matcher built: 6 pattern(s)
[2026-09-08T15:17:52.076Z] INFO [aft-pi] [aft] 2026-09-08T15:17:52Z [aft] search index orphan sweep root=~/.local/share/cortexkit/aft/index scanned=31 removed=0 skipped_derived=1 skipped_memo=29 skipped_fresh=1 skipped_live=0 skipped_locked=0 skipped_unreadable=0 budget_exhausted=false
[2026-09-08T15:17:52.077Z] INFO [aft-pi] [aft] 2026-09-08T15:17:52Z [aft] transient search cache sweep root=/tmp scanned=0 removed=0 bytes=0 skipped_fresh=0 skipped_unreadable=0 budget_exhausted=false
[2026-09-08T15:17:52.078Z] INFO [aft-pi] [aft] 2026-09-08T15:17:52Z [aft] watcher stopped: ~/Projects/github.com/spice-labs-inc/app-gitops
[2026-09-08T15:17:52.110Z] INFO [aft-pi] [aft] 2026-09-08T15:17:52Z [aft] watcher started: ~/Projects/github.com/spice-labs-inc/app-gitops
[2026-09-08T15:18:15.349Z] INFO [aft-pi] Process exited during shutdown
[2026-09-08T15:18:15.349Z] INFO [aft-pi] Bridge pool shut down
[2026-09-08T15:18:31.176Z] INFO [aft-pi] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-08T15:18:31.178Z] INFO [aft-pi] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-08T15:18:31.178Z] INFO [aft-pi] AFT extension loading (plugin v0.55.1)
[2026-09-08T15:18:31.216Z] INFO [aft-pi] Resolved binary from versioned cache: ~/.cache/aft/bin/v0.55.1/aft
[2026-09-08T15:18:31.217Z] INFO [aft-pi] AFT storage already migrated for pi; using ~/.local/share/cortexkit/aft
[2026-09-08T15:18:31.314Z] INFO [aft-pi] ONNX Runtime found at ~/.local/share/cortexkit/aft/onnxruntime/1.24.4 (TOFU verified)
[2026-09-08T15:18:31.316Z] INFO [aft-pi] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-08T15:18:31.835Z] INFO [aft-pi] [lsp] auto-install: 1 npm + 0 github install(s) running in background
[2026-09-08T15:18:31.841Z] INFO [aft-pi] Workflow hints injected (5064 chars)
[2026-09-08T15:18:31.841Z] INFO [aft-pi] AFT extension ready (surface=all)
[2026-09-08T15:18:31.841Z] INFO [aft-pi] ONNX Runtime ready at ~/.local/share/cortexkit/aft/onnxruntime/1.24.4; new bridges will load semantic backend.
[2026-09-08T15:18:31.842Z] INFO [aft-pi] Spawning binary: ~/.cache/aft/bin/v0.55.1/aft (cwd: ~/Projects/github.com/spice-labs-inc/basil)
[2026-09-08T15:18:31.843Z] INFO [aft-pi] bridge.spawnProcess: useFastembedBackend=true, parentORT=(unset), ortLibraryPath=~/.local/share/cortexkit/aft/onnxruntime/1.24.4/libonnxruntime.so
[2026-09-08T15:18:31.843Z] INFO [aft-pi] ORT_DYLIB_PATH set from managed ONNX Runtime: ~/.local/share/cortexkit/aft/onnxruntime/1.24.4/libonnxruntime.so
[2026-09-08T15:18:32.215Z] INFO [aft-pi] hashline registration carrier transport=ndjson phase=configure edit_slot_survives=false
[2026-09-08T15:18:32.342Z] INFO [aft-pi] [aft] 2026-09-08T15:18:32Z [aft] log retention sweep: removed_files=0 bytes_freed=0
[2026-09-08T15:18:32.343Z] INFO [aft-pi] [aft] 2026-09-08T15:18:32Z [aft] started, pid 706863
[2026-09-08T15:18:32.343Z] INFO [aft-pi] [aft] 2026-09-08T15:18:32Z [aft] project root set: ~/Projects/github.com/spice-labs-inc/basil
[2026-09-08T15:18:32.343Z] INFO [aft-pi] [aft] 2026-09-08T15:18:32Z [aft] gitignore matcher built: 7 pattern(s)
[2026-09-08T15:18:32.343Z] INFO [aft-pi] [aft] 2026-09-08T15:18:32Z [aft] search index orphan sweep root=~/.local/share/cortexkit/aft/index scanned=31 removed=0 skipped_derived=1 skipped_memo=29 skipped_fresh=1 skipped_live=0 skipped_locked=0 skipped_unreadable=0 budget_exhausted=false
[2026-09-08T15:18:32.343Z] INFO [aft-pi] [aft] 2026-09-08T15:18:32Z [aft] transient search cache sweep root=/tmp scanned=0 removed=0 bytes=0 skipped_fresh=0 skipped_unreadable=0 budget_exhausted=false
[2026-09-08T15:18:32.343Z] INFO [aft-pi] [aft] 2026-09-08T15:18:32Z [aft] quarantining unresolved background task bash-84319d597c5c02c2: background task layout not found
[2026-09-08T15:18:32.343Z] INFO [aft-pi] [aft] 2026-09-08T15:18:32Z [aft] loaded symbol cache from disk: 38 files
[2026-09-08T15:18:32.343Z] INFO [aft-pi] [aft] 2026-09-08T15:18:32Z [aft] pre-warmed symbol cache: 0 new, 38 cached, 38 files total
[2026-09-08T15:18:32.343Z] INFO [aft-pi] [aft] 2026-09-08T15:18:32Z [aft] callgraph store warm deferred until semantic cold seed gate clears or completes
[2026-09-08T15:18:32.873Z] INFO [aft-pi] [aft] 2026-09-08T15:18:32Z [aft] cannot establish filesystem boundary for checkpoint sweep ~/.local/share/cortexkit/aft/pi/checkpoints
[2026-09-08T15:18:32.873Z] INFO [aft-pi] [aft] 2026-09-08T15:18:32Z [aft] watcher started: ~/Projects/github.com/spice-labs-inc/basil
[2026-09-08T15:18:32.873Z] INFO [aft-pi] [aft] 2026-09-08T15:18:32Z [aft] local embedder ready: model=all-MiniLM-L6-v2 intra_threads=36 token_type_ids=<REDACTED_SECRET>
[2026-09-08T15:18:32.873Z] INFO [aft-pi] [aft] 2026-09-08T15:18:32Z [aft] loaded semantic index from disk: 351 entries
[2026-09-08T15:18:32.873Z] INFO [aft-pi] [aft] 2026-09-08T15:18:32Z [aft] semantic index: cached index is current (351 entries)
[2026-09-08T15:18:32.874Z] INFO [aft-pi] Binary version: 0.55.1
[2026-09-08T15:18:32.927Z] INFO [aft-pi] [aft] 2026-09-08T15:18:32Z [aft] project root set: ~/Projects/github.com/spice-labs-inc/basil
[2026-09-08T15:18:32.928Z] INFO [aft-pi] [lsp] lsp_paths_extra updated after auto-install: 10 dirs pushed to live bridges
[2026-09-08T15:18:32.931Z] INFO [aft-pi] [aft] 2026-09-08T15:18:32Z [aft] gitignore matcher built: 7 pattern(s)
[2026-09-08T15:18:32.932Z] INFO [aft-pi] [aft] 2026-09-08T15:18:32Z [aft] search index orphan sweep root=~/.local/share/cortexkit/aft/index scanned=31 removed=0 skipped_derived=1 skipped_memo=29 skipped_fresh=1 skipped_live=0 skipped_locked=0 skipped_unreadable=0 budget_exhausted=false
[2026-09-08T15:18:32.933Z] INFO [aft-pi] [aft] 2026-09-08T15:18:32Z [aft] transient search cache sweep root=/tmp scanned=0 removed=0 bytes=0 skipped_fresh=0 skipped_unreadable=0 budget_exhausted=false
[2026-09-08T15:18:32.944Z] INFO [aft-pi] [aft] 2026-09-08T15:18:32Z [aft] watcher stopped: ~/Projects/github.com/spice-labs-inc/basil
[2026-09-08T15:18:33.312Z] INFO [aft-pi] [aft] 2026-09-08T15:18:33Z [aft] watcher started: ~/Projects/github.com/spice-labs-inc/basil
[2026-09-08T15:18:46.686Z] INFO [aft-pi] Process exited during shutdown
[2026-09-08T15:18:46.686Z] INFO [aft-pi] Bridge pool shut down
[2026-09-08T15:19:08.438Z] INFO [aft-pi] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-08T15:19:08.440Z] INFO [aft-pi] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-08T15:19:08.440Z] INFO [aft-pi] AFT extension loading (plugin v0.55.1)
[2026-09-08T15:19:08.500Z] INFO [aft-pi] Resolved binary from versioned cache: ~/.cache/aft/bin/v0.55.1/aft
[2026-09-08T15:19:08.500Z] INFO [aft-pi] AFT storage already migrated for pi; using ~/.local/share/cortexkit/aft
[2026-09-08T15:19:08.600Z] INFO [aft-pi] ONNX Runtime found at ~/.local/share/cortexkit/aft/onnxruntime/1.24.4 (TOFU verified)
[2026-09-08T15:19:08.602Z] INFO [aft-pi] Config loaded from ~/.config/cortexkit/aft.jsonc
[2026-09-08T15:19:09.139Z] INFO [aft-pi] [lsp] auto-install: 1 npm + 0 github install(s) running in background
[2026-09-08T15:19:09.140Z] INFO [aft-pi] Workflow hints injected (5064 chars)
[2026-09-08T15:19:09.140Z] INFO [aft-pi] AFT extension ready (surface=all)
[2026-09-08T15:19:09.140Z] INFO [aft-pi] ONNX Runtime ready at ~/.local/share/cortexkit/aft/onnxruntime/1.24.4; new bridges will load semantic backend.
[2026-09-08T15:19:09.141Z] INFO [aft-pi] Spawning binary: ~/.cache/aft/bin/v0.55.1/aft (cwd: ~/Projects/github.com/spice-labs-inc/basil)
[2026-09-08T15:19:09.141Z] INFO [aft-pi] bridge.spawnProcess: useFastembedBackend=true, parentORT=(unset), ortLibraryPath=~/.local/share/cortexkit/aft/onnxruntime/1.24.4/libonnxruntime.so
[2026-09-08T15:19:09.141Z] INFO [aft-pi] ORT_DYLIB_PATH set from managed ONNX Runtime: ~/.local/share/cortexkit/aft/onnxruntime/1.24.4/libonnxruntime.so
[2026-09-08T15:19:09.520Z] INFO [aft-pi] hashline registration carrier transport=ndjson phase=configure edit_slot_survives=false
[2026-09-08T15:19:09.544Z] INFO [aft-pi] [aft] 2026-09-08T15:19:09Z [aft] log retention sweep: removed_files=0 bytes_freed=0
[2026-09-08T15:19:09.544Z] INFO [aft-pi] [aft] 2026-09-08T15:19:09Z [aft] started, pid 708417
[2026-09-08T15:19:10.198Z] INFO [aft-pi] [aft] 2026-09-08T15:19:09Z [aft] project root set: ~/Projects/github.com/spice-labs-inc/basil
[2026-09-08T15:19:10.198Z] INFO [aft-pi] [aft] 2026-09-08T15:19:09Z [aft] gitignore matcher built: 7 pattern(s)
[2026-09-08T15:19:10.198Z] INFO [aft-pi] [aft] 2026-09-08T15:19:09Z [aft] search index orphan sweep root=~/.local/share/cortexkit/aft/index scanned=31 removed=0 skipped_derived=1 skipped_memo=29 skipped_fresh=1 skipped_live=0 skipped_locked=0 skipped_unreadable=0 budget_exhausted=false
[2026-09-08T15:19:10.198Z] INFO [aft-pi] [aft] 2026-09-08T15:19:09Z [aft] transient search cache sweep root=/tmp scanned=0 removed=0 bytes=0 skipped_fresh=0 skipped_unreadable=0 budget_exhausted=false
[2026-09-08T15:19:10.198Z] INFO [aft-pi] [aft] 2026-09-08T15:19:09Z [aft] quarantining unresolved background task bash-84319d597c5c02c2: background task layout not found
[2026-09-08T15:19:10.199Z] INFO [aft-pi] [aft] 2026-09-08T15:19:09Z [aft] loaded symbol cache from disk: 38 files
[2026-09-08T15:19:10.199Z] INFO [aft-pi] [aft] 2026-09-08T15:19:09Z [aft] pre-warmed symbol cache: 0 new, 38 cached, 38 files total
[2026-09-08T15:19:10.199Z] INFO [aft-pi] [aft] 2026-09-08T15:19:09Z [aft] callgraph store warm deferred until semantic cold seed gate clears or completes
[2026-09-08T15:19:10.199Z] INFO [aft-pi] [aft] 2026-09-08T15:19:09Z [aft] cannot establish filesystem boundary for checkpoint sweep ~/.local/share/cortexkit/aft/pi/checkpoints
[2026-09-08T15:19:10.199Z] INFO [aft-pi] [aft] 2026-09-08T15:19:09Z [aft] watcher started: ~/Projects/github.com/spice-labs-inc/basil
[2026-09-08T15:19:10.199Z] INFO [aft-pi] [aft] 2026-09-08T15:19:09Z [aft] local embedder ready: model=all-MiniLM-L6-v2 intra_threads=36 token_type_ids=<REDACTED_SECRET>
[2026-09-08T15:19:10.199Z] INFO [aft-pi] [aft] 2026-09-08T15:19:10Z [aft] loaded semantic index from disk: 351 entries
[2026-09-08T15:19:10.199Z] INFO [aft-pi] [aft] 2026-09-08T15:19:10Z [aft] semantic index: cached index is current (351 entries)
[2026-09-08T15:19:10.240Z] INFO [aft-pi] [aft] 2026-09-08T15:19:10Z [aft] project root set: ~/Projects/github.com/spice-labs-inc/basil
[2026-09-08T15:19:10.240Z] INFO [aft-pi] [aft] 2026-09-08T15:19:10Z [aft] gitignore matcher built: 7 pattern(s)
[2026-09-08T15:19:10.240Z] INFO [aft-pi] [aft] 2026-09-08T15:19:10Z [aft] search index orphan sweep root=~/.local/share/cortexkit/aft/index scanned=31 removed=0 skipped_derived=1 skipped_memo=29 skipped_fresh=1 skipped_live=0 skipped_locked=0 skipped_unreadable=0 budget_exhausted=false
[2026-09-08T15:19:10.240Z] INFO [aft-pi] [aft] 2026-09-08T15:19:10Z [aft] transient search cache sweep root=/tmp scanned=0 removed=0 bytes=0 skipped_fresh=0 skipped_unreadable=0 budget_exhausted=false
[2026-09-08T15:19:10.240Z] INFO [aft-pi] [aft] 2026-09-08T15:19:10Z [aft] watcher stopped: ~/Projects/github.com/spice-labs-inc/basil
[2026-09-08T15:19:10.240Z] INFO [aft-pi] [lsp] lsp_paths_extra updated after auto-install: 10 dirs pushed to live bridges
[2026-09-08T15:19:10.247Z] INFO [aft-pi] Binary version: 0.55.1
[2026-09-08T15:19:10.573Z] INFO [aft-pi] [aft] 2026-09-08T15:19:10Z [aft] watcher started: ~/Projects/github.com/spice-labs-inc/basil
[2026-09-08T15:19:10.905Z] INFO [aft-pi] [aft] 2026-09-08T15:19:10Z [aft] [ses_01a08199-aa74-766e-8c1d-0be5e7b2aca3] bash_wait_detach: session=01a08199-aa74-766e-8c1d-0be5e7b2aca3 detached=false active_wait_sessions=0
[2026-09-08T15:19:15.238Z] INFO [aft-pi] [01a08199-aa74-766e-8c1d-0be5e7b2aca3] [aft-pi] bg-notifications: drain ok {"event":"bash_completion_drain_ok","count":0,"task_ids":[],"canonical_root":"~/Projects/github.com/spice-labs-inc/basil","suppressed":0}
[2026-09-08T15:20:09.598Z] INFO [aft-pi] [aft] 2026-09-08T15:20:09Z [aft] [ses_01a08199-aa74-766e-8c1d-0be5e7b2aca3] 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

Usernames and home paths have been stripped from this report.

[aft-alfonso]

Thanks - two things are visible in this report, and both are ours.

1. The issue body itself got cut: everything you typed before </system-reminder> is missing, because npx @cortexkit/aft doctor --issue pasted your description into a Markdown template that treats that tag as markup. That is a doctor bug; fixing it so the description is fenced verbatim.

2. The reminder that repeats on every Pi reopen looks like a durable background-completion notice for a task whose bundle is gone (the log shows quarantining unresolved background task bash-84319d597c5c02c2: background task layout not found on every start). Completions re-arm until the host acknowledges them, so if the acknowledgement never lands on Pi the same [BG BASH NOTIFY] is re-injected each session. To confirm from your side, could you paste the exact reminder text you see (the <system-reminder> [BG BASH NOTIFY] ... block), and the output of aft_status or a bash_status call on bash-e3d611742251... if the agent can run it? I am reproducing the reopen loop on Pi with an erased-bundle pending completion in the meantime.

[aredridel]

Restored cut-off text.

[aft-alfonso]

Thanks for restoring the text - that names it exactly. The repeating notice is a pattern-watch tombstone (watch target erased: a bash_watch was armed on bash-e3d611742251a573 and the task was erased before the watch reached a normal end), not a task completion, and my first reproduction only covered the completion case. The tombstone is supposed to be delivered once and then acknowledged away; on your build it is surviving the acknowledgement across restarts. Reproducing that specific row shape now and will report the mechanism and the release that carries the fix here. In the meantime it is harmless beyond the noise; if you want it gone immediately, npx @cortexkit/aft doctor --clear resets the background-task store.

[aft-alfonso]

Mechanism found and fixed on main, reproduced against an archived 0.55.1 binary:

• The tombstone (watch target erased) is acknowledged away only when the daemon's predicate says the watched task is gone, and on 0.55.1 that predicate required the task's database row to be absent. A quarantined task keeps its row (only the on-disk layout is moved aside), so the acknowledgement never cleared the watch row and it re-tombstoned on every restart. Fixed: an acknowledged tombstone is deleted regardless of whether the task row survived.
• On 0.55.1 the Pi plugin also delivered watch-only notices without acknowledging them at all (it acknowledged task completions, not pattern-watch frames), so even a correct predicate would not have helped that build. Main already acknowledges them; both paths now have restart-twice regressions.

No tagged release contains both fixes yet; the next release cut from main does. Until then npx @cortexkit/aft doctor --clear clears the store if the notice bothers you. Thanks for the clean report - the restored text is what named the row.

[aft-alfonso]

One more change from your report, now on main: a session no longer receives background-task notices for tasks it did not start. Previously a new session bound to the same project inherited every earlier session's pending notices (by design, so a build that finished after you closed the host wasn't lost) - which is how a fresh Pi got a tombstone for a task from before pi update. That inheritance is gone; earlier sessions' tasks stay visible to bash_status/kill by id, but their notices are delivered only to the session that started them, and orphaned ones are retired quietly. Ships with the next release together with the acknowledgement fix above.

[iceteaSA]

Traced this on v0.55.1 (source refs below are from a fork at that tag; symbols are stable, line numbers may drift a little against upstream main). Not reproduced end-to-end here — this is a source trace, so treat the mechanism as the claim and the repro as still open.

Short version: the tombstone row is emitted on a channel that carries no ack marker, and the only thing preventing re-emission is process-local. So it repeats forever.

The loop

1. evaluate_erased_watch_targets (bash_background/registry.rs:998) finds a persisted watch row whose task row is gone and writes a tombstone (pending_match=true, match_text=WATCH_TARGET_ERASED_TEXT). Note :1053 pushes the notification outside the if !already_tombstoned block, so an already-tombstoned row notifies again on every pass.
2. The only redelivery guard is WatchRegistry::terminalize_erased_task (watches.rs:193) inserting into erased_notifications — an in-memory HashSet (watches.rs:80). It is never persisted, and restore (watches.rs:107-139) does not repopulate it, so it is empty on every process start. That is the restart half the reporter is seeing.
3. The persisted row is deleted only in ack_completions_for_session (registry.rs:3120), in the branch gated on has_erased_watch_reference (registry.rs:979, branch at :3147-3172).

Why that branch can't be reached

has_erased_watch_reference requires list_bash_tasks_by_id to be empty — the task row is gone by definition. But the ack only ever receives task ids that came back from a drain, and drain_completions_for_session (registry.rs:3092-3106) returns inner.completions filtered by session. An erased task has no completion, so its id can never appear in the drained set, and both plugins derive their ack list from bg_completions (pi bg-notifications.ts:801-804, opencode 1003-1006).

The erased notice instead ships as a bash_pattern_match frame (protocol.rs:399-417). Plugins only turn a pattern match into an ack when ackCompletionOnDelivery is set (pi bg-notifications.ts:1167, opencode 1411) — and BashPatternMatchFrame (protocol.rs:88-100) has no such field. The flag is only ever set by completionToExitPattern (pi :1138-1157), which synthesizes entries from real completions. So the daemon-pushed tombstone is rendered and never acked.

Worth noting: drain_completions_for_session calls redeliver_pending_watches_for_session first (:3094), and for an erased row that routes to emit_bash_watch_erased (registry.rs:938) — another push, adding nothing to completions. So the notice re-fires on every drain, not only on restart.

Net: the cleanup branch at registry.rs:3147-3172 looks like it was written for exactly this case, but nothing on the wire can trigger it.

Constraints on a fix

• Don't just move the push inside !already_tombstoned, and don't just persist the dedup set. watches.rs:107-110 documents that scanning=false rows are deliberately retained so a pending match can be redelivered until acked; both of those silently kill legitimate cross-restart redelivery of a genuinely unacked watch.
• Don't key a plugin-side ack on reason === "task_exit" alone — the locally synthesized completion entries use that same reason (pi :1154). The discriminator is match_text == WATCH_TARGET_ERASED_TEXT, or the real watch_id vs the synthetic "exit".
• Connecting the existing seam (an ack marker on the erased frame, so the plugin's existing ack path reaches has_erased_watch_reference) preserves redelivery-until-ack; deleting the row at emit time does not.

Test gap

pattern_watch_acked_match_does_not_redeliver_after_restart (registry.rs:8472-8547) covers an acknowledged genuine match, and pattern_watch_rows_become_pending_tombstones_when_task_is_gc_deleted (:8628-8700) covers tombstone retention — but I found nothing covering erased-watch redelivery across a restart, which is the reported symptom. Happy to put up a PR if the fix direction above is the one you want.

[aft-alfonso]

Thanks @iceteaSA - that matches what the reproduction found and adds two facts I did not have. Confirmed against current main:

• evaluate_erased_watch_targets still pushes the notification outside the already_tombstoned block (registry.rs:1135), and WatchRegistry::erased_notifications is still an in-process HashSet, so the once-per-process dedupe does not survive a restart. On 0.55.1 that plus the unreachable cleanup branch is the whole loop; your every-drain observation (redeliver_pending_watches_for_session -> emit_bash_watch_erased) is the within-session half the reporter also saw.
• What closes it on main: the cleanup branch no longer needs the task row to be absent (it keys on the row being in tombstone state), so an acknowledgement deletes the watch row; both plugins now acknowledge pattern-match frames, not only completions (so something on the wire can reach that branch); and as of today notices are delivered only to the session that started the task, so a fresh session bound to the same project never inherits an earlier session's tombstone in the first place (orphaned rows are retired on replay). With the row deleted on ack, the process-local dedupe only has to hold within one process, which it does.

Restart-twice regressions cover the surviving-row and gone-row variants, the Pi watch-only ack, and the foreign-session cases. All on main, none released yet - next release.