Merge pull request #20 from ngallodev/sync/upstream-step5

Sync upstream step 5: merge 84 new upstream commits (96c3f41..268a9d8) into the CLI fork

Author: ngallodev

.github/workflows/codeql.yml

@@ -29,7 +29,7 @@ jobs:
         run: sudo apt-get update && sudo apt-get install -y zlib1g-dev
 
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@b96794f015dfd88f77b49b1c93e0fa7110f94c63 # v4.38.0
+        uses: github/codeql-action/init@1c5b675653bb5c22dbe9b12b556ec555138e09fd # v4.38.1
         with:
           languages: c-cpp
           build-mode: manual
@@ -38,6 +38,6 @@ jobs:
         run: scripts/build.sh
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@b96794f015dfd88f77b49b1c93e0fa7110f94c63 # v4.38.0
+        uses: github/codeql-action/analyze@1c5b675653bb5c22dbe9b12b556ec555138e09fd # v4.38.1
         with:
           category: "/language:c-cpp"

.github/workflows/scorecard.yml

@@ -27,6 +27,6 @@ jobs:
           publish_results: true
 
       - name: Upload SARIF results
-        uses: github/codeql-action/upload-sarif@b96794f015dfd88f77b49b1c93e0fa7110f94c63 # v4
+        uses: github/codeql-action/upload-sarif@1c5b675653bb5c22dbe9b12b556ec555138e09fd # v4
         with:
           sarif_file: results.sarif

Makefile.cbm

@@ -341,6 +341,7 @@ FOUNDATION_SRCS = \
 EXTRACTION_SRCS = \
     $(CBM_DIR)/cbm.c \
     $(CBM_DIR)/extract_defs.c \
+    $(CBM_DIR)/callable_sig.c \
     $(CBM_DIR)/extract_calls.c \
     $(CBM_DIR)/extract_imports.c \
     $(CBM_DIR)/extract_usages.c \
@@ -438,6 +439,7 @@ PIPELINE_SRCS = \
     src/pipeline/lsp_surface.c \
     src/pipeline/pipeline_delta.c \
     src/pipeline/path_alias.c \
+    src/pipeline/laravel_routing.c \
     src/pipeline/registry.c \
     src/pipeline/pipeline.c \
     src/pipeline/pipeline_incremental.c \
@@ -637,6 +639,7 @@ TEST_FOUNDATION_OBJS = $(patsubst %.c,$(BUILD_DIR)/%.test.o,$(TEST_FOUNDATION_SR
 
 TEST_EXTRACTION_SRCS = \
     tests/test_extraction.c \
+    tests/test_callable_sig.c \
     tests/test_extraction_inheritance.c \
     tests/test_extraction_imports.c \
     tests/test_parse_coverage.c \

README.md

@@ -337,3 +337,5 @@ See [`SECURITY.md`](SECURITY.md) and [`docs/SECURITY-DISCLOSURE.md`](docs/SECURI
 ## License and upstream attribution
 
 MIT. The root [`LICENSE`](LICENSE) preserves the upstream `Copyright (c) 2025 DeusData` notice. See [`UPSTREAM_ATTRIBUTION.md`](UPSTREAM_ATTRIBUTION.md) for the explicit distinction between inherited DeusData work and modifications made in this fork.
+
+Uninstall keeps project indexes by default, including with `--yes`, `--no`, or noninteractive input. Use `--delete-indexes` to remove them explicitly; `--dry-run` previews the changes.

docs/CONFIGURATION.md

@@ -88,6 +88,7 @@ Current keys:
 | `auto_index` | `false` | Permit the retained warm runtime to auto-index newly encountered projects. Canonical CLI usage can always index explicitly with `codebase-memory-cli index`. |
 | `auto_index_limit` | `50000` | Maximum file count allowed for automatic indexing of a new project. |
 | `auto_watch` | `true` | Register an active project with the retained background watcher when a warm runtime/hook integration supplies project context. The ordinary one-shot CLI does not require this. |
+| `watch_non_git` | `false` | Poll non-Git roots with the indexer discovery rules and an adaptive file-tree scan. Skipped paths, including `.codebase-memory/`, do not trigger indexing. The first poll after daemon startup reindexes once; later changes trigger one reindex. This walks the whole tree each poll and is read when the daemon starts. |
 | `watcher_enabled` | `true` | Master switch for the retained background watcher subsystem. Set `false` to stop its poll thread/project registration. Reindex manually with `codebase-memory-cli index` when disabled. |
 | `index_max_files` | `off` | Optional maximum number of accepted source files in one discovery run. |
 | `index_max_source_mb` | `off` | Optional maximum accepted source size in MiB in one discovery run. |

install.ps1

@@ -320,81 +320,102 @@ try {
 
 $Dest = Join-Path $InstallDir $BinName
 
-# Retire the running installation before replacing it. Windows keeps an image
-# lock on a running .exe: the file cannot be overwritten, but it CAN be renamed
-# out of the way, which is what makes an in-place update possible from here.
-if (Test-Path -LiteralPath $Dest -PathType Leaf) {
-    try { & $Dest daemon stop 2>&1 | Out-Null } catch { }
-    $retired = "$Dest.retired-$(Get-Date -Format yyyyMMddHHmmss)"
-    $renamed = $false
-    foreach ($attempt in 1..10) {
-        try { Move-Item -LiteralPath $Dest -Destination $retired -Force -ErrorAction Stop; $renamed = $true; break }
-        catch { Start-Sleep -Milliseconds 500 }
+$retired = $null
+$ActivationSucceeded = $false
+try {
+    # Retire the running installation before replacing it. Windows keeps an image
+    # lock on a running .exe: the file cannot be overwritten, but it CAN be renamed
+    # out of the way, which is what makes an in-place update possible from here.
+    if (Test-Path -LiteralPath $Dest -PathType Leaf) {
+        try { & $Dest daemon stop 2>&1 | Out-Null } catch { }
+        $retired = "$Dest.retired-$([Guid]::NewGuid().ToString('N'))"
+        $renamed = $false
+        foreach ($attempt in 1..10) {
+            try { Move-Item -LiteralPath $Dest -Destination $retired -ErrorAction Stop; $renamed = $true; break }
+            catch { Start-Sleep -Milliseconds 500 }
+        }
+        if (-not $renamed) {
+            Write-Host "error: could not retire the existing $BinName - close all running" -ForegroundColor Red
+            Write-Host "       codebase-memory-cli sessions and coding agents, then re-run." -ForegroundColor Red
+            Remove-Item -Recurse -Force $TmpDir -ErrorAction SilentlyContinue
+            exit 1
+        }
+        # Keep the old image until activation and the installed-binary probe succeed.
     }
-    if (-not $renamed) {
-        Write-Host "error: could not retire the existing $BinName - close all running" -ForegroundColor Red
-        Write-Host "       codebase-memory-cli sessions and coding agents, then re-run." -ForegroundColor Red
+
+    $InstallArgs = @("install", "-y", "--force", "--dir=$InstallDir")
+    if ($SkipConfig) { $InstallArgs += "--skip-config" }
+    & $DownloadedBinary @InstallArgs
+    if ($LASTEXITCODE -ne 0) {
+        Write-Host "error: installation failed (exit code $LASTEXITCODE)" -ForegroundColor Red
         Remove-Item -Recurse -Force $TmpDir -ErrorAction SilentlyContinue
         exit 1
     }
-    # A retired image stays locked until its last process exits; delete it when
-    # we can, and leave it for the next run when we cannot. Never fail here.
-    Remove-Item -LiteralPath $retired -Force -ErrorAction SilentlyContinue
-}
-Get-ChildItem -LiteralPath $InstallDir -Filter "$BinName.retired-*" -ErrorAction SilentlyContinue |
-    ForEach-Object { Remove-Item -LiteralPath $_.FullName -Force -ErrorAction SilentlyContinue }
 
-$InstallArgs = @("install", "-y", "--force", "--dir=$InstallDir")
-if ($SkipConfig) { $InstallArgs += "--skip-config" }
-& $DownloadedBinary @InstallArgs
-if ($LASTEXITCODE -ne 0) {
-    Write-Host "error: installation failed (exit code $LASTEXITCODE)" -ForegroundColor Red
-    Remove-Item -Recurse -Force $TmpDir -ErrorAction SilentlyContinue
-    exit 1
-}
+    # Place the installer beside the binary so `update` points at a local file
+    # rather than a URL, and so the next update runs THIS release's installer.
+    #
+    # Sourced from the archive we just checksum-verified, and published by rename
+    # rather than written over the live path. PowerShell parses a script fully
+    # before executing it, so self-overwrite is less hazardous here than it is for
+    # bash -- but rename costs nothing and keeps both platforms on one rule.
+    # Best effort: a failure here still leaves a working install.
+    $DownloadedInstaller = Join-Path $TmpDir "install.ps1"
+    if (Test-Path -LiteralPath $DownloadedInstaller -PathType Leaf) {
+        $InstallerDest = Join-Path $InstallDir "install.ps1"
+        $InstallerTmp = "$InstallerDest.new"
+        try {
+            Copy-Item -LiteralPath $DownloadedInstaller -Destination $InstallerTmp -Force -ErrorAction Stop
+            Move-Item -LiteralPath $InstallerTmp -Destination $InstallerDest -Force -ErrorAction Stop
+            Write-Host "Installed updater -> $InstallerDest"
+        } catch {
+            Remove-Item -LiteralPath $InstallerTmp -Force -ErrorAction SilentlyContinue
+            Write-Host "note: could not place install.ps1 in $InstallDir (update will explain where to find it)"
+        }
+    }
 
-# Place the installer beside the binary so `update` points at a local file
-# rather than a URL, and so the next update runs THIS release's installer.
-#
-# Sourced from the archive we just checksum-verified, and published by rename
-# rather than written over the live path. PowerShell parses a script fully
-# before executing it, so self-overwrite is less hazardous here than it is for
-# bash -- but rename costs nothing and keeps both platforms on one rule.
-# Best effort: a failure here still leaves a working install.
-$DownloadedInstaller = Join-Path $TmpDir "install.ps1"
-if (Test-Path -LiteralPath $DownloadedInstaller -PathType Leaf) {
-    $InstallerDest = Join-Path $InstallDir "install.ps1"
-    $InstallerTmp = "$InstallerDest.new"
+    # Verify
+    # Same PS 5.1 stderr-wrapping guard as the candidate probe above; the pre-seed
+    # matters MOST here, because prior successful native calls leave a stale
+    # $LASTEXITCODE=0 that a start-failure would otherwise inherit.
     try {
-        Copy-Item -LiteralPath $DownloadedInstaller -Destination $InstallerTmp -Force -ErrorAction Stop
-        Move-Item -LiteralPath $InstallerTmp -Destination $InstallerDest -Force -ErrorAction Stop
-        Write-Host "Installed updater -> $InstallerDest"
+        $ProbeEap = $ErrorActionPreference
+        try {
+            $ErrorActionPreference = "Continue"
+            $global:LASTEXITCODE = 1
+            $ver = & $Dest --version 2>&1
+        } finally {
+            $ErrorActionPreference = $ProbeEap
+        }
+        if ($LASTEXITCODE -ne 0) { throw "installed binary exited with $LASTEXITCODE" }
+        Write-Host "Installed: $ver"
     } catch {
-        Remove-Item -LiteralPath $InstallerTmp -Force -ErrorAction SilentlyContinue
-        Write-Host "note: could not place install.ps1 in $InstallDir (update will explain where to find it)"
+        Write-Host "error: installed binary failed to run" -ForegroundColor Red
+        Remove-Item -Recurse -Force $TmpDir
+        exit 1
     }
-}
 
-# Verify
-# Same PS 5.1 stderr-wrapping guard as the candidate probe above; the pre-seed
-# matters MOST here, because prior successful native calls leave a stale
-# $LASTEXITCODE=0 that a start-failure would otherwise inherit.
-try {
-    $ProbeEap = $ErrorActionPreference
-    try {
-        $ErrorActionPreference = "Continue"
-        $global:LASTEXITCODE = 1
-        $ver = & $Dest --version 2>&1
-    } finally {
-        $ErrorActionPreference = $ProbeEap
+    $ActivationSucceeded = $true
+} finally {
+    if (-not $ActivationSucceeded -and $retired -and
+        (Test-Path -LiteralPath $retired -PathType Leaf)) {
+        if (-not (Test-Path -LiteralPath $Dest)) {
+            try {
+                Move-Item -LiteralPath $retired -Destination $Dest -ErrorAction Stop
+            } catch {
+                Write-Host "error: could not restore $Dest; previous binary retained at $retired : $_" -ForegroundColor Red
+            }
+        } else {
+            # The inner activation may deliberately retain a published candidate
+            # after partial config/PATH changes. Do not override that decision or
+            # overwrite an unexpected path entry outside its activation lease.
+            Write-Host "note: keeping the published executable; previous binary retained at $retired"
+        }
     }
-    if ($LASTEXITCODE -ne 0) { throw "installed binary exited with $LASTEXITCODE" }
-    Write-Host "Installed: $ver"
-} catch {
-    Write-Host "error: installed binary failed to run" -ForegroundColor Red
-    Remove-Item -Recurse -Force $TmpDir
-    exit 1
 }
+# Retired images are disposable only after the replacement has been verified.
+Get-ChildItem -LiteralPath $InstallDir -Filter "$BinName.retired-*" -ErrorAction SilentlyContinue |
+    ForEach-Object { Remove-Item -LiteralPath $_.FullName -Force -ErrorAction SilentlyContinue }
 
 # Agent configuration was included in the candidate-owned activation window.
 if ($SkipConfig) {