Semantic search not working outside of project's root

[tenshiak]

Short description

aft_search times out when searching outside of project's root, even when it's indexed

What happened?

When my LLM tries to use aft_search across projects, where both were indexed by aft, it times out and throws this error.

callgraph also fails, but right away, throwing an error that searching outside of root is unsupported. Even though both were indexed by aft

Additional information.: Both projects were opened by two different docker containers sharing the same aft database location, but a different aft process. Both have access to /shared/pi_source. The second one opened pi inside this folder. I ran it only in /shared/pi_source first and made sure it's done working before starting it in ~/pi to make sure there are no races. I even deleted the whole aft database to make sure it starts from a clean slate.

It doesn't work from one way, but does the other.
From inside ~/.pi can't aft_search inside /shared/pi_source - bridge busy error
From inside /shared/pi_source can aft_search inside ~/.pi
~/.pi of course can use aft_search inside ~/.pi

Diagnostics

## Environment
- AFT CLI: v0.46.0
- AFT binary: 0.46.0
- OS: linux x64
- Node: v24.18.0

## Diagnostics
- Timestamp: 2026-07-09T20:23:06.052Z
- AFT CLI: v0.46.0
- AFT binary: 0.46.0
- OS: linux x64
- Node: v24.18.0

### Pi
- Host installed: true
- Host version: 0.80.5
- Plugin registered: true
- Plugin version: not installed
- AFT enabled: true (from ~/.config/cortexkit/aft.jsonc)
- 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

{
  "$schema": "https://raw.githubusercontent.com/cortexkit/aft/main/assets/aft.schema.json",
  "enabled": true,
  "hoist_builtin_tools": true,
  "format_on_edit": true,
  "validate_on_edit": "syntax",
  "formatter": {
    "typescript": "biome",
    "python": "ruff",
    "rust": "rustfmt"
  },
  "checker": {
    "typescript": "biome"
  },
  "configure_warnings_delivery": "toast",
  "tool_surface": "all",
  "disabled_tools": [
    "aft_conflicts",
    "aft_import",
    "aft_delete",
    "aft_move",
    "aft_refactor"
  ],
  "search_index": true,
  "semantic_search": true,
  "semantic": {
    "backend": "fastembed",
    "model": "all-MiniLM-L6-v2",
    "timeout_ms": 25000,
    "max_batch_size": 64,
    "max_files": 20000
  },
  "restrict_to_project_root": false,
  "auto_update": false,
  "lsp": {
    "auto_install": false,
    "servers": {},
    "disabled": [
      "typescript"
    ],
    "python": "ty"
  },
  "bash": {
    "rewrite": false,
    "compress": false,
    "background": false,
    "subagent_background": false,
    "foreground_wait_window_ms": 8000
  },
  "inspect": {
    "enabled": true,
    "tier2_idle_minutes": 5
  },
  "backup": {
    "enabled": true
  }
}


#### Plugin cache

{
  "path": "~/.pi/agent/extensions",
  "exists": false
}


#### Storage

{
  "path": "~/.local/share/cortexkit/aft",
  "exists": true,
  "accessible": true,
  "sizesByKey": {
    "index": 10607482,
    "semantic": 200986439,
    "backups": 0,
    "url_cache": 39213,
    "onnxruntime": 66492548
  }
}


#### ONNX Runtime

{
  "required": true,
  "systemPath": null,
  "systemVersion": null,
  "systemCompatible": 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
`/tmp/aft-pi.log` (55 KB)

### Binary cache

{
  "versions": [
    "v0.46.0"
  ],
  "activeVersion": "v0.46.0",
  "totalSize": 75291360,
  "path": "~/.cache/aft/bin"
}


### LSP cache

{
  "npm": {
    "path": "~/.cache/aft/lsp-packages",
    "entries": [],
    "totalSize": 0
  },
  "github": {
    "path": "~/.cache/aft/lsp-binaries",
    "entries": [],
    "totalSize": 0
  },
  "totalSize": 0
}


## Recent errors (last 20, sanitized)

[2026-07-09T19:46:13.528Z] WARN [aft-pi] [019f4868-7c92-7799-b3ff-965552b28274] [aft-pi] bg-notifications: drain failed: [aft-pi] Request "bash_drain_completions" (id=5) timed out after 30000ms
[2026-07-09T19:48:17.623Z] WARN [aft-pi] [019f4868-7c92-7799-b3ff-965552b28274] [aft-pi] bg-notifications: drain failed: [aft-pi] Request "bash_drain_completions" (id=12) timed out after 30000ms
[2026-07-09T19:49:52.303Z] WARN [aft-pi] [019f4868-7c92-7799-b3ff-965552b28274] [aft-pi] bg-notifications: drain failed: [aft-pi] Request "bash_drain_completions" (id=16) timed out after 30000ms
[2026-07-09T19:56:08.020Z] WARN [aft-pi] [019f4871-5cde-7755-b193-95c29be6ac70] [aft-pi] bg-notifications: drain failed: [aft-pi] Request "bash_drain_completions" (id=5) timed out after 30000ms
[2026-07-09T20:18:32.866Z] WARN [aft-pi] [019f4883-227c-7523-addc-66bfe420808f] [aft-pi] bg-notifications: drain failed: [aft-pi] Request "bash_drain_completions" (id=9) timed out after 30000ms


### Recent AFT tool failures
No recent AFT tool failures recorded.

## Logs (last 200 lines per harness)
#### Pi log (/tmp/aft-pi.log)


[2026-07-09T19:53:39.778Z] INFO [aft-pi] ONNX Runtime found at ~/.local/share/cortexkit/aft/onnxruntime/1.24.4 (TOFU verified)
[2026-07-09T19:53:40.122Z] INFO [aft-pi] Workflow hints injected (3364 chars)
[2026-07-09T19:53:40.122Z] INFO [aft-pi] AFT extension ready (surface=all)
[2026-07-09T19:53:40.122Z] INFO [aft-pi] ONNX Runtime ready at ~/.local/share/cortexkit/aft/onnxruntime/1.24.4; new bridges will load semantic backend.
[2026-07-09T19:53:40.124Z] INFO [aft-pi] Spawning binary: ~/.cache/aft/bin/v0.46.0/aft (cwd: <PROJECT>)
[2026-07-09T19:53:40.124Z] INFO [aft-pi] bridge.spawnProcess: useFastembedBackend=true, parentORT=(unset), ortLibraryPath=~/.local/share/cortexkit/aft/onnxruntime/1.24.4/libonnxruntime.so
[2026-07-09T19:53:40.124Z] INFO [aft-pi] ORT_DYLIB_PATH set from managed ONNX Runtime: ~/.local/share/cortexkit/aft/onnxruntime/1.24.4/libonnxruntime.so
[2026-07-09T19:53:41.904Z] INFO [aft-pi] [aft] started, pid 27
[2026-07-09T19:53:41.938Z] INFO [aft-pi] [aft] project root set: <PROJECT>
[2026-07-09T19:53:41.980Z] INFO [aft-pi] [aft] acquired filesystem lock at ~/.local/share/cortexkit/aft/index/ceb11238169701bf/cache.lock
[2026-07-09T19:53:42.204Z] INFO [aft-pi] [aft] loaded 13 backup entries across 8 session(s) from disk
[2026-07-09T19:53:42.493Z] INFO [aft-pi] [aft] gitignore matcher built: 38 pattern(s)
[2026-07-09T19:53:42.516Z] INFO [aft-pi] [aft] failed to open aft.db at ~/.local/share/cortexkit/aft/aft.db: sqlite error: disk I/O error — running with JSON-only persistence
[2026-07-09T19:53:42.870Z] INFO [aft-pi] [aft] callgraph store warm deferred until semantic cold seed gate clears or completes
[2026-07-09T19:53:42.923Z] INFO [aft-pi] Binary version: 0.46.0
[2026-07-09T19:53:43.095Z] INFO [aft-pi] [aft] local embedder ready: model=all-MiniLM-L6-v2 intra_threads=8 token_type_ids=<REDACTED_SECRET>
[2026-07-09T19:53:43.180Z] INFO [aft-pi] [aft] acquired filesystem lock at ~/.local/share/cortexkit/aft/semantic/ceb11238169701bf/cache.lock
[2026-07-09T19:53:43.511Z] INFO [aft-pi] [aft] search index: refreshed 5 stale file(s) from disk cache
[2026-07-09T19:53:43.516Z] INFO [aft-pi] [aft] released filesystem lock at ~/.local/share/cortexkit/aft/index/ceb11238169701bf/cache.lock
[2026-07-09T19:53:43.940Z] INFO [aft-pi] [aft] loaded symbol cache from disk: 105 files
[2026-07-09T19:53:44.054Z] INFO [aft-pi] [aft] acquired filesystem lock at ~/.local/share/cortexkit/aft/symbols/ceb11238169701bf/symbols.lock
[2026-07-09T19:53:44.100Z] INFO [aft-pi] [aft] released filesystem lock at ~/.local/share/cortexkit/aft/symbols/ceb11238169701bf/symbols.lock
[2026-07-09T19:53:44.100Z] INFO [aft-pi] [aft] persisted symbol cache: 105 files
[2026-07-09T19:53:44.100Z] INFO [aft-pi] [aft] pre-warmed symbol cache: 0 new, 105 cached, 105 files total
[2026-07-09T19:53:45.683Z] INFO [aft-pi] [aft] loaded semantic index from disk: 575 entries
[2026-07-09T19:53:46.054Z] INFO [aft-pi] [aft] semantic index: cached index is current (575 entries)
[2026-07-09T19:53:46.060Z] INFO [aft-pi] [aft] released filesystem lock at ~/.local/share/cortexkit/aft/semantic/ceb11238169701bf/cache.lock
[2026-07-09T19:53:46.899Z] INFO [aft-pi] [aft] tier2 refresh scheduled: reason=pull, categories=["dead_code", "unused_exports", "duplicates", "cycles"]
[2026-07-09T19:53:53.644Z] INFO [aft-pi] [aft] tier2 dead_code: refreshed callgraph store at ~/.local/share/cortexkit/aft/pi/callgraph for 4 watcher path(s): changed=4 deleted=0 refreshed_own=0
[2026-07-09T19:53:53.667Z] INFO [aft-pi] [aft] tier2 dead_code: callgraph store projection unavailable at ~/.local/share/cortexkit/aft/pi/callgraph (callgraph has stale files pending refresh); trying fallback=false
[2026-07-09T19:53:53.668Z] INFO [aft-pi] [aft] tier2 dead_code: no ready callgraph store found for inspect_dir ~/.local/share/cortexkit/aft/pi/inspect; reporting callgraph_unavailable
[2026-07-09T19:53:57.337Z] INFO [aft-pi] [aft] tier2 dead_code: refreshed callgraph store at ~/.local/share/cortexkit/aft/pi/callgraph for 4 watcher path(s): changed=4 deleted=0 refreshed_own=0
[2026-07-09T19:53:57.360Z] INFO [aft-pi] [aft] tier2 dead_code: callgraph store projection unavailable at ~/.local/share/cortexkit/aft/pi/callgraph (callgraph has stale files pending refresh); trying fallback=false
[2026-07-09T19:53:57.363Z] INFO [aft-pi] [aft] tier2 dead_code: no ready callgraph store found for inspect_dir ~/.local/share/cortexkit/aft/pi/inspect; reporting callgraph_unavailable
[2026-07-09T19:53:57.388Z] INFO [aft-pi] [aft] perf tier2 phases category=dead_code freshness=141ms snapshot=8450ms scan=0ms(4 files) db=518ms rollup=25ms
[2026-07-09T19:53:57.388Z] INFO [aft-pi] [aft] perf tier2 category=dead_code reuse=miss ms=10489
[2026-07-09T19:55:22.790Z] INFO [aft-pi] [aft] watcher started: <PROJECT>
[2026-07-09T19:55:38.018Z] WARN [aft-pi] [019f4871-5cde-7755-b193-95c29be6ac70] Request "tool_call" (id=4) timed out after 60000ms — bridge kept warm
[2026-07-09T19:56:08.019Z] WARN [aft-pi] [019f4871-5cde-7755-b193-95c29be6ac70] Request "bash_drain_completions" (id=5) timed out after 30000ms — restarting bridge
[2026-07-09T19:56:08.020Z] ERROR [aft-pi] [019f4871-5cde-7755-b193-95c29be6ac70] Bridge killed after timeout.
  --- last 20 stderr lines ---
  [aft] search index: refreshed 5 stale file(s) from disk cache
  [aft] released filesystem lock at ~/.local/share/cortexkit/aft/index/ceb11238169701bf/cache.lock
  [aft] loaded symbol cache from disk: 105 files
  [aft] acquired filesystem lock at ~/.local/share/cortexkit/aft/symbols/ceb11238169701bf/symbols.lock
  [aft] released filesystem lock at ~/.local/share/cortexkit/aft/symbols/ceb11238169701bf/symbols.lock
  [aft] persisted symbol cache: 105 files
  [aft] pre-warmed symbol cache: 0 new, 105 cached, 105 files total
  [aft] loaded semantic index from disk: 575 entries
  [aft] semantic index: cached index is current (575 entries)
  [aft] released filesystem lock at ~/.local/share/cortexkit/aft/semantic/ceb11238169701bf/cache.lock
  [aft] tier2 refresh scheduled: reason=pull, categories=["dead_code", "unused_exports", "duplicates", "cycles"]
  [aft] tier2 dead_code: refreshed callgraph store at ~/.local/share/cortexkit/aft/pi/callgraph for 4 watcher path(s): changed=4 deleted=0 refreshed_own=0
  [aft] tier2 dead_code: callgraph store projection unavailable at ~/.local/share/cortexkit/aft/pi/callgraph (callgraph has stale files pending refresh); trying fallback=false
  [aft] tier2 dead_code: no ready callgraph store found for inspect_dir ~/.local/share/cortexkit/aft/pi/inspect; reporting callgraph_unavailable
  [aft] tier2 dead_code: refreshed callgraph store at ~/.local/share/cortexkit/aft/pi/callgraph for 4 watcher path(s): changed=4 deleted=0 refreshed_own=0
  [aft] tier2 dead_code: callgraph store projection unavailable at ~/.local/share/cortexkit/aft/pi/callgraph (callgraph has stale files pending refresh); trying fallback=false
  [aft] tier2 dead_code: no ready callgraph store found for inspect_dir ~/.local/share/cortexkit/aft/pi/inspect; reporting callgraph_unavailable
  [aft] perf tier2 phases category=dead_code freshness=141ms snapshot=8450ms scan=0ms(4 files) db=518ms rollup=25ms
  [aft] perf tier2 category=dead_code reuse=miss ms=10489
  [aft] watcher started: <PROJECT>
[2026-07-09T19:56:08.020Z] WARN [aft-pi] [019f4871-5cde-7755-b193-95c29be6ac70] [aft-pi] bg-notifications: drain failed: [aft-pi] Request "bash_drain_completions" (id=5) timed out after 30000ms
[2026-07-09T19:56:08.023Z] INFO [aft-pi] [019f4871-5cde-7755-b193-95c29be6ac70] Spawning binary: ~/.cache/aft/bin/v0.46.0/aft (cwd: <PROJECT>)
[2026-07-09T19:56:08.023Z] INFO [aft-pi] bridge.spawnProcess: useFastembedBackend=true, parentORT=(unset), ortLibraryPath=~/.local/share/cortexkit/aft/onnxruntime/1.24.4/libonnxruntime.so
[2026-07-09T19:56:08.023Z] INFO [aft-pi] ORT_DYLIB_PATH set from managed ONNX Runtime: ~/.local/share/cortexkit/aft/onnxruntime/1.24.4/libonnxruntime.so
[2026-07-09T19:56:08.116Z] INFO [aft-pi] [aft] started, pid 200
[2026-07-09T19:56:09.598Z] INFO [aft-pi] [aft] [ses_019f4871-5cde-7755-b193-95c29be6ac70] project root set: <PROJECT>
[2026-07-09T19:56:09.635Z] INFO [aft-pi] [aft] [ses_019f4871-5cde-7755-b193-95c29be6ac70] acquired filesystem lock at ~/.local/share/cortexkit/aft/index/ceb11238169701bf/cache.lock
[2026-07-09T19:56:09.801Z] INFO [aft-pi] [aft] [ses_019f4871-5cde-7755-b193-95c29be6ac70] loaded 13 backup entries across 8 session(s) from disk
[2026-07-09T19:56:10.156Z] INFO [aft-pi] [aft] [ses_019f4871-5cde-7755-b193-95c29be6ac70] gitignore matcher built: 38 pattern(s)
[2026-07-09T19:56:10.186Z] INFO [aft-pi] [aft] [ses_019f4871-5cde-7755-b193-95c29be6ac70] failed to open aft.db at ~/.local/share/cortexkit/aft/aft.db: sqlite error: disk I/O error — running with JSON-only persistence
[2026-07-09T19:56:10.552Z] INFO [aft-pi] [aft] [ses_019f4871-5cde-7755-b193-95c29be6ac70] callgraph store warm deferred until semantic cold seed gate clears or completes
[2026-07-09T19:56:10.594Z] INFO [aft-pi] Binary version: 0.46.0
[2026-07-09T19:56:10.734Z] INFO [aft-pi] [aft] [ses_019f4871-5cde-7755-b193-95c29be6ac70] local embedder ready: model=all-MiniLM-L6-v2 intra_threads=8 token_type_ids=<REDACTED_SECRET>
[2026-07-09T19:56:10.801Z] INFO [aft-pi] [aft] [ses_019f4871-5cde-7755-b193-95c29be6ac70] acquired filesystem lock at ~/.local/share/cortexkit/aft/semantic/ceb11238169701bf/cache.lock
[2026-07-09T19:56:10.891Z] INFO [aft-pi] [aft] [ses_019f4871-5cde-7755-b193-95c29be6ac70] search index: refreshed 5 stale file(s) from disk cache
[2026-07-09T19:56:10.896Z] INFO [aft-pi] [aft] [ses_019f4871-5cde-7755-b193-95c29be6ac70] released filesystem lock at ~/.local/share/cortexkit/aft/index/ceb11238169701bf/cache.lock
[2026-07-09T19:56:11.310Z] INFO [aft-pi] [aft] [ses_019f4871-5cde-7755-b193-95c29be6ac70] loaded symbol cache from disk: 105 files
[2026-07-09T19:56:11.420Z] INFO [aft-pi] [aft] [ses_019f4871-5cde-7755-b193-95c29be6ac70] acquired filesystem lock at ~/.local/share/cortexkit/aft/symbols/ceb11238169701bf/symbols.lock
[2026-07-09T19:56:11.464Z] INFO [aft-pi] [aft] [ses_019f4871-5cde-7755-b193-95c29be6ac70] released filesystem lock at ~/.local/share/cortexkit/aft/symbols/ceb11238169701bf/symbols.lock
[2026-07-09T19:56:11.464Z] INFO [aft-pi] [aft] [ses_019f4871-5cde-7755-b193-95c29be6ac70] persisted symbol cache: 105 files
[2026-07-09T19:56:11.464Z] INFO [aft-pi] [aft] [ses_019f4871-5cde-7755-b193-95c29be6ac70] pre-warmed symbol cache: 0 new, 105 cached, 105 files total
[2026-07-09T19:56:12.539Z] INFO [aft-pi] [aft] [ses_019f4871-5cde-7755-b193-95c29be6ac70] loaded semantic index from disk: 575 entries
[2026-07-09T19:56:12.889Z] INFO [aft-pi] [aft] [ses_019f4871-5cde-7755-b193-95c29be6ac70] semantic index: cached index is current (575 entries)
[2026-07-09T19:56:12.898Z] INFO [aft-pi] [aft] [ses_019f4871-5cde-7755-b193-95c29be6ac70] released filesystem lock at ~/.local/share/cortexkit/aft/semantic/ceb11238169701bf/cache.lock
[2026-07-09T19:56:13.795Z] INFO [aft-pi] [aft] [ses_019f4871-5cde-7755-b193-95c29be6ac70] tier2 refresh scheduled: reason=pull, categories=["dead_code", "unused_exports", "duplicates", "cycles"]
[2026-07-09T20:13:04.300Z] WARN [aft-pi] Config validation error in ~/.config/cortexkit/aft.jsonc: : Unrecognized keys: "hoist_builtin_tools", "auto_update"
[2026-07-09T20:13:04.321Z] WARN [aft-pi] Config validation error in ~/.config/cortexkit/aft.jsonc: : Unrecognized keys: "hoist_builtin_tools", "auto_update"
[2026-07-09T20:13:04.322Z] INFO [aft-pi] AFT extension loading (plugin v0.46.0)
[2026-07-09T20:13:04.362Z] INFO [aft-pi] Resolved binary: ~/.cache/aft/bin/v0.46.0/aft
[2026-07-09T20:13:04.365Z] INFO [aft-pi] AFT storage migration skipped for pi: no legacy data at ~/.pi/agent/aft; using ~/.local/share/cortexkit/aft for fresh install
[2026-07-09T20:13:04.539Z] INFO [aft-pi] ONNX Runtime found at ~/.local/share/cortexkit/aft/onnxruntime/1.24.4 (TOFU verified)
[2026-07-09T20:13:04.904Z] INFO [aft-pi] Workflow hints injected (3364 chars)
[2026-07-09T20:13:04.905Z] INFO [aft-pi] AFT extension ready (surface=all)
[2026-07-09T20:13:04.905Z] INFO [aft-pi] ONNX Runtime ready at ~/.local/share/cortexkit/aft/onnxruntime/1.24.4; new bridges will load semantic backend.
[2026-07-09T20:13:04.906Z] INFO [aft-pi] Spawning binary: ~/.cache/aft/bin/v0.46.0/aft (cwd: <PROJECT>)
[2026-07-09T20:13:04.906Z] INFO [aft-pi] bridge.spawnProcess: useFastembedBackend=true, parentORT=(unset), ortLibraryPath=~/.local/share/cortexkit/aft/onnxruntime/1.24.4/libonnxruntime.so
[2026-07-09T20:13:04.906Z] INFO [aft-pi] ORT_DYLIB_PATH set from managed ONNX Runtime: ~/.local/share/cortexkit/aft/onnxruntime/1.24.4/libonnxruntime.so
[2026-07-09T20:13:06.819Z] INFO [aft-pi] [aft] started, pid 21
[2026-07-09T20:13:06.819Z] INFO [aft-pi] [aft] project root set: <PROJECT>
[2026-07-09T20:13:06.819Z] INFO [aft-pi] [aft] acquired filesystem lock at ~/.local/share/cortexkit/aft/index/ceb11238169701bf/cache.lock
[2026-07-09T20:13:06.819Z] INFO [aft-pi] [aft] loaded 13 backup entries across 8 session(s) from disk
[2026-07-09T20:13:06.819Z] INFO [aft-pi] [aft] gitignore matcher built: 38 pattern(s)
[2026-07-09T20:13:06.819Z] INFO [aft-pi] [aft] failed to open aft.db at ~/.local/share/cortexkit/aft/aft.db: sqlite error: disk I/O error — running with JSON-only persistence
[2026-07-09T20:13:07.140Z] INFO [aft-pi] [aft] callgraph store warm deferred until semantic cold seed gate clears or completes
[2026-07-09T20:13:07.160Z] INFO [aft-pi] Binary version: 0.46.0
[2026-07-09T20:13:07.480Z] INFO [aft-pi] [aft] local embedder ready: model=all-MiniLM-L6-v2 intra_threads=8 token_type_ids=<REDACTED_SECRET>
[2026-07-09T20:13:07.579Z] INFO [aft-pi] [aft] acquired filesystem lock at ~/.local/share/cortexkit/aft/semantic/ceb11238169701bf/cache.lock
[2026-07-09T20:13:07.824Z] INFO [aft-pi] [aft] search index cold streaming build: 123 files, 19634 trigrams, 1722 ms (pool=8)
[2026-07-09T20:13:08.119Z] INFO [aft-pi] [aft] semantic collect: 575 chunks from 43 files in 69 ms
[2026-07-09T20:13:13.548Z] INFO [aft-pi] [aft] released filesystem lock at ~/.local/share/cortexkit/aft/index/ceb11238169701bf/cache.lock
[2026-07-09T20:13:13.549Z] INFO [aft-pi] [aft] loaded symbol cache from disk: 0 files
[2026-07-09T20:13:14.526Z] INFO [aft-pi] [aft] acquired filesystem lock at ~/.local/share/cortexkit/aft/symbols/ceb11238169701bf/symbols.lock
[2026-07-09T20:13:14.574Z] INFO [aft-pi] [aft] released filesystem lock at ~/.local/share/cortexkit/aft/symbols/ceb11238169701bf/symbols.lock
[2026-07-09T20:13:14.574Z] INFO [aft-pi] [aft] persisted symbol cache: 105 files
[2026-07-09T20:13:14.574Z] INFO [aft-pi] [aft] pre-warmed symbol cache: 105 new, 0 cached, 105 files total
[2026-07-09T20:13:15.785Z] INFO [aft-pi] [aft] semantic embed: 575 chunks in 9 batches, 7668 ms (74 chunks/s)
[2026-07-09T20:13:15.785Z] INFO [aft-pi] [aft] built semantic index: 43 files, 575 entries
[2026-07-09T20:13:15.899Z] INFO [aft-pi] [aft] semantic index persisted: 575 entries, 1222.9 KB
[2026-07-09T20:13:15.905Z] INFO [aft-pi] [aft] released filesystem lock at ~/.local/share/cortexkit/aft/semantic/ceb11238169701bf/cache.lock
[2026-07-09T20:13:16.503Z] INFO [aft-pi] [aft] deferred callgraph store warm scheduled after semantic cold seed gate cleared
[2026-07-09T20:13:16.511Z] INFO [aft-pi] [aft] tier2 refresh scheduled: reason=pull, categories=["dead_code", "unused_exports", "duplicates", "cycles"]
[2026-07-09T20:13:16.987Z] INFO [aft-pi] [aft] acquired filesystem lock at ~/.local/share/cortexkit/aft/pi/callgraph/ceb11238169701bf.build.lock
[2026-07-09T20:13:18.152Z] INFO [aft-pi] [aft] tier2 dead_code: callgraph store unavailable at ~/.local/share/cortexkit/aft/pi/callgraph (cold/building/not ready); trying fallback=false
[2026-07-09T20:13:18.152Z] INFO [aft-pi] [aft] tier2 dead_code: no ready callgraph store found for inspect_dir ~/.local/share/cortexkit/aft/pi/inspect; reporting callgraph_unavailable
[2026-07-09T20:13:20.042Z] INFO [aft-pi] [aft] tier2 dead_code: callgraph store unavailable at ~/.local/share/cortexkit/aft/pi/callgraph (cold/building/not ready); trying fallback=false
[2026-07-09T20:13:20.042Z] INFO [aft-pi] [aft] tier2 dead_code: no ready callgraph store found for inspect_dir ~/.local/share/cortexkit/aft/pi/inspect; reporting callgraph_unavailable
[2026-07-09T20:13:20.054Z] INFO [aft-pi] [aft] perf tier2 phases category=dead_code freshness=0ms snapshot=1133ms scan=0ms(105 files) db=579ms rollup=12ms
[2026-07-09T20:13:20.054Z] INFO [aft-pi] [aft] perf tier2 category=dead_code reuse=miss ms=3543
[2026-07-09T20:13:23.206Z] INFO [aft-pi] [aft] perf callgraph_store cold_build (chunked): files=105 <USER>s=1050 refs=4040 edges=1162 ms=5742
[2026-07-09T20:13:23.330Z] INFO [aft-pi] [aft] released filesystem lock at ~/.local/share/cortexkit/aft/pi/callgraph/ceb11238169701bf.build.lock
[2026-07-09T20:13:27.501Z] INFO [aft-pi] [aft] perf tier2 phases category=unused_exports freshness=0ms snapshot=0ms scan=3845ms(105 files) db=569ms rollup=2434ms
[2026-07-09T20:13:27.501Z] INFO [aft-pi] [aft] perf tier2 category=unused_exports reuse=miss ms=7446
[2026-07-09T20:13:28.576Z] INFO [aft-pi] [aft] perf tier2 phases category=duplicates freshness=0ms snapshot=0ms scan=142ms(105 files) db=363ms rollup=16ms
[2026-07-09T20:13:28.576Z] INFO [aft-pi] [aft] perf tier2 category=duplicates reuse=miss ms=1074
[2026-07-09T20:13:33.614Z] INFO [aft-pi] [aft] perf tier2 phases category=cycles freshness=0ms snapshot=0ms scan=3068ms(105 files) db=508ms rollup=945ms
[2026-07-09T20:13:33.614Z] INFO [aft-pi] [aft] perf tier2 category=cycles reuse=miss ms=5032
[2026-07-09T20:14:42.107Z] INFO [aft-pi] [aft] watcher started: <PROJECT>
[2026-07-09T20:15:16.128Z] INFO [aft-pi] [aft] [ses_019f4883-227c-7523-addc-66bfe420808f] local embedder ready: model=all-MiniLM-L6-v2 intra_threads=8 token_type_ids=<REDACTED_SECRET>
[2026-07-09T20:16:32.353Z] WARN [aft-pi] [019f4883-227c-7523-addc-66bfe420808f] Request "tool_call" (id=6) timed out after 60000ms — bridge kept warm
[2026-07-09T20:16:52.772Z] INFO [aft-pi] [aft] [ses_019f4883-227c-7523-addc-66bfe420808f] loaded semantic index from disk: 8029 entries
[2026-07-09T20:18:02.865Z] WARN [aft-pi] [019f4883-227c-7523-addc-66bfe420808f] Request "tool_call" (id=8) timed out after 60000ms — bridge kept warm
[2026-07-09T20:18:32.864Z] WARN [aft-pi] [019f4883-227c-7523-addc-66bfe420808f] Request "bash_drain_completions" (id=9) timed out after 30000ms — restarting bridge
[2026-07-09T20:18:32.866Z] ERROR [aft-pi] [019f4883-227c-7523-addc-66bfe420808f] Bridge killed after timeout.
  --- last 20 stderr lines ---
  [aft] deferred callgraph store warm scheduled after semantic cold seed gate cleared
  [aft] tier2 refresh scheduled: reason=pull, categories=["dead_code", "unused_exports", "duplicates", "cycles"]
  [aft] acquired filesystem lock at ~/.local/share/cortexkit/aft/pi/callgraph/ceb11238169701bf.build.lock
  [aft] tier2 dead_code: callgraph store unavailable at ~/.local/share/cortexkit/aft/pi/callgraph (cold/building/not ready); trying fallback=false
  [aft] tier2 dead_code: no ready callgraph store found for inspect_dir ~/.local/share/cortexkit/aft/pi/inspect; reporting callgraph_unavailable
  [aft] tier2 dead_code: callgraph store unavailable at ~/.local/share/cortexkit/aft/pi/callgraph (cold/building/not ready); trying fallback=false
  [aft] tier2 dead_code: no ready callgraph store found for inspect_dir ~/.local/share/cortexkit/aft/pi/inspect; reporting callgraph_unavailable
  [aft] perf tier2 phases category=dead_code freshness=0ms snapshot=1133ms scan=0ms(105 files) db=579ms rollup=12ms
  [aft] perf tier2 category=dead_code reuse=miss ms=3543
  [aft] perf callgraph_store cold_build (chunked): files=105 <USER>s=1050 refs=4040 edges=1162 ms=5742
  [aft] released filesystem lock at ~/.local/share/cortexkit/aft/pi/callgraph/ceb11238169701bf.build.lock
  [aft] perf tier2 phases category=unused_exports freshness=0ms snapshot=0ms scan=3845ms(105 files) db=569ms rollup=2434ms
  [aft] perf tier2 category=unused_exports reuse=miss ms=7446
  [aft] perf tier2 phases category=duplicates freshness=0ms snapshot=0ms scan=142ms(105 files) db=363ms rollup=16ms
  [aft] perf tier2 category=duplicates reuse=miss ms=1074
  [aft] perf tier2 phases category=cycles freshness=0ms snapshot=0ms scan=3068ms(105 files) db=508ms rollup=945ms
  [aft] perf tier2 category=cycles reuse=miss ms=5032
  [aft] watcher started: <PROJECT>
  [aft] [ses_019f4883-227c-7523-addc-66bfe420808f] local embedder ready: model=all-MiniLM-L6-v2 intra_threads=8 token_type_ids=<REDACTED_SECRET>
  [aft] [ses_019f4883-227c-7523-addc-66bfe420808f] loaded semantic index from disk: 8029 entries
[2026-07-09T20:18:32.866Z] WARN [aft-pi] [019f4883-227c-7523-addc-66bfe420808f] [aft-pi] bg-notifications: drain failed: [aft-pi] Request "bash_drain_completions" (id=9) timed out after 30000ms
[2026-07-09T20:19:38.062Z] INFO [aft-pi] [019f4883-227c-7523-addc-66bfe420808f] Spawning binary: ~/.cache/aft/bin/v0.46.0/aft (cwd: <PROJECT>)
[2026-07-09T20:19:38.062Z] INFO [aft-pi] bridge.spawnProcess: useFastembedBackend=true, parentORT=(unset), ortLibraryPath=~/.local/share/cortexkit/aft/onnxruntime/1.24.4/libonnxruntime.so
[2026-07-09T20:19:38.062Z] INFO [aft-pi] ORT_DYLIB_PATH set from managed ONNX Runtime: ~/.local/share/cortexkit/aft/onnxruntime/1.24.4/libonnxruntime.so
[2026-07-09T20:19:38.146Z] INFO [aft-pi] [aft] started, pid 263
[2026-07-09T20:19:39.562Z] INFO [aft-pi] [aft] [ses_019f4883-227c-7523-addc-66bfe420808f] project root set: <PROJECT>
[2026-07-09T20:19:39.602Z] INFO [aft-pi] [aft] [ses_019f4883-227c-7523-addc-66bfe420808f] acquired filesystem lock at ~/.local/share/cortexkit/aft/index/ceb11238169701bf/cache.lock
[2026-07-09T20:19:39.778Z] INFO [aft-pi] [aft] [ses_019f4883-227c-7523-addc-66bfe420808f] loaded 13 backup entries across 8 session(s) from disk
[2026-07-09T20:19:40.137Z] INFO [aft-pi] [aft] [ses_019f4883-227c-7523-addc-66bfe420808f] gitignore matcher built: 38 pattern(s)
[2026-07-09T20:19:40.167Z] INFO [aft-pi] [aft] [ses_019f4883-227c-7523-addc-66bfe420808f] failed to open aft.db at ~/.local/share/cortexkit/aft/aft.db: sqlite error: disk I/O error — running with JSON-only persistence
[2026-07-09T20:19:40.531Z] INFO [aft-pi] [aft] [ses_019f4883-227c-7523-addc-66bfe420808f] callgraph store warm deferred until semantic cold seed gate clears or completes
[2026-07-09T20:19:40.552Z] INFO [aft-pi] Binary version: 0.46.0
[2026-07-09T20:19:40.726Z] INFO [aft-pi] [aft] [ses_019f4883-227c-7523-addc-66bfe420808f] local embedder ready: model=all-MiniLM-L6-v2 intra_threads=8 token_type_ids=<REDACTED_SECRET>
[2026-07-09T20:19:40.791Z] INFO [aft-pi] [aft] [ses_019f4883-227c-7523-addc-66bfe420808f] acquired filesystem lock at ~/.local/share/cortexkit/aft/semantic/ceb11238169701bf/cache.lock
[2026-07-09T20:19:40.850Z] INFO [aft-pi] [aft] [ses_019f4883-227c-7523-addc-66bfe420808f] search index: refreshed 1 stale file(s) from disk cache
[2026-07-09T20:19:40.855Z] INFO [aft-pi] [aft] [ses_019f4883-227c-7523-addc-66bfe420808f] released filesystem lock at ~/.local/share/cortexkit/aft/index/ceb11238169701bf/cache.lock
[2026-07-09T20:19:41.306Z] INFO [aft-pi] [aft] [ses_019f4883-227c-7523-addc-66bfe420808f] loaded symbol cache from disk: 104 files
[2026-07-09T20:19:41.444Z] INFO [aft-pi] [aft] [ses_019f4883-227c-7523-addc-66bfe420808f] acquired filesystem lock at ~/.local/share/cortexkit/aft/symbols/ceb11238169701bf/symbols.lock
[2026-07-09T20:19:41.484Z] INFO [aft-pi] [aft] [ses_019f4883-227c-7523-addc-66bfe420808f] released filesystem lock at ~/.local/share/cortexkit/aft/symbols/ceb11238169701bf/symbols.lock
[2026-07-09T20:19:41.484Z] INFO [aft-pi] [aft] [ses_019f4883-227c-7523-addc-66bfe420808f] persisted symbol cache: 105 files
[2026-07-09T20:19:41.484Z] INFO [aft-pi] [aft] [ses_019f4883-227c-7523-addc-66bfe420808f] pre-warmed symbol cache: 1 new, 104 cached, 105 files total
[2026-07-09T20:19:42.575Z] INFO [aft-pi] [aft] [ses_019f4883-227c-7523-addc-66bfe420808f] loaded semantic index from disk: 575 entries
[2026-07-09T20:19:42.970Z] INFO [aft-pi] [aft] [ses_019f4883-227c-7523-addc-66bfe420808f] semantic index: cached index is current (575 entries)
[2026-07-09T20:19:42.976Z] INFO [aft-pi] [aft] [ses_019f4883-227c-7523-addc-66bfe420808f] released filesystem lock at ~/.local/share/cortexkit/aft/semantic/ceb11238169701bf/cache.lock
[2026-07-09T20:19:43.956Z] INFO [aft-pi] [aft] [ses_019f4883-227c-7523-addc-66bfe420808f] tier2 refresh scheduled: reason=pull, categories=["dead_code", "unused_exports", "duplicates", "cycles"]
[2026-07-09T20:19:46.723Z] INFO [aft-pi] [aft] perf tier2_callgraph_snapshot: source=callgraph_store files=105 exports=214 edges=3829 entry_points=3 ms=1616
[2026-07-09T20:20:02.531Z] INFO [aft-pi] [aft] perf tier2 phases category=dead_code freshness=0ms snapshot=1617ms scan=9007ms(105 files) db=592ms rollup=6201ms
[2026-07-09T20:20:02.531Z] INFO [aft-pi] [aft] perf tier2 category=dead_code reuse=miss ms=18577
[2026-07-09T20:20:07.675Z] INFO [aft-pi] [aft] perf tier2 phases category=unused_exports freshness=150ms snapshot=0ms scan=1138ms(1 files) db=498ms rollup=2574ms
[2026-07-09T20:20:07.675Z] INFO [aft-pi] [aft] perf tier2 category=unused_exports reuse=miss ms=5142
[2026-07-09T20:20:08.693Z] INFO [aft-pi] [aft] perf tier2 phases category=duplicates freshness=129ms snapshot=0ms scan=5ms(1 files) db=228ms rollup=11ms
[2026-07-09T20:20:08.693Z] INFO [aft-pi] [aft] perf tier2 category=duplicates reuse=miss ms=1016
[2026-07-09T20:20:10.427Z] INFO [aft-pi] [aft] perf tier2 phases category=cycles freshness=153ms snapshot=0ms scan=429ms(1 files) db=449ms rollup=0ms
[2026-07-09T20:20:10.427Z] INFO [aft-pi] [aft] perf tier2 category=cycles reuse=miss ms=1728
[2026-07-09T20:21:17.868Z] INFO [aft-pi] [aft] watcher started: <PROJECT>


_Usernames and home paths have been stripped from this report._

Plugin version

No response

AFT binary version

No response

Platform

No response

Log output (optional)

[alfonso-aft]

Thanks for the detailed report — the log pins it. When aft_search targets another project, loading that project's index currently runs inline on the engine's request thread, and in your setup (shared storage on a docker volume, cross-container) that load is slow enough to blow the 60s call timeout and take the engine down with it — that's the "bridge busy" you saw afterwards. Fix in progress: cross-project index loads move to the background with a quick "loading, retry" response, and the freshness check gets much cheaper on the borrow path (borrowed results already disclose drift, so byte-exact verification is unnecessary there). The direction asymmetry is just which side has the bigger index to verify.

One expected behavior in the mix: aft_callgraph is project-scoped by design — only aft_search supports cross-project queries — but the error message will say that properly instead of a flat refusal.

Also noted your aft.db disk I/O error: SQLite on a container-shared volume isn't safe for locking; AFT degrades to JSON-only persistence when that happens, which is why everything else kept working.

[tenshiak]

Would it be possible to add support for a full-fledged centralized database like PostgreSQL or MariaDB? I imagine I'm not the only one in the world that uses/will use aft and magic context inside containers.