0.6.11: Auto-apply exact-tag format upgrades; self-heal stale pending rows

Two gaps left obvious cases stuck in the manual dedup queue:

1. Format-upgrade pairs found by Pass 2/3 (case-insensitive/normalized
   tag match) still required manual confirm even though the pass
   itself already proved same song via identical tags, and rank_file()
   already guarantees FLAC beats any other format regardless of
   size/dirty-name. A directory-casing difference (e.g. "All About
   This Ep" vs "...EP") meant these never matched the narrower
   same-directory numbered-twin rule from 0.6.10. New is_format_upgrade()
   auto-deletes any Pass 2/3 pair whose extensions differ, gated on
   pass_name so Pass 4 (cross-album fuzzy -- different masters, DJ-mix
   edits, genuinely ambiguous) is untouched and still requires a human.

2. A pending row can go stale without ever being confirmed -- some
   other action (a later auto-apply, upgrade-mp3-to-flac, a manual fix)
   already resolved one side of the pair -- and nothing pruned it, so
   an already-fixed duplicate kept surfacing in the queue indefinitely.
   scan() now sweeps and auto-resolves any pending candidate whose
   keep_path or delete_path no longer exists before persisting new
   ones, so the queue reflects current reality on every run instead of
   accumulating dead entries.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

README.md

@@ -73,10 +73,10 @@ Optional, add these later if you want them:
 Pull the prebuilt image onto your Docker host:
 
 ```bash
-docker pull git.kretzer.club/andrew/alembic:0.6.9
+docker pull git.kretzer.club/andrew/alembic:0.6.11
 ```
 
-That is the whole install. You do not need to download the source or build anything. The `0.6.9` is the version; you can pin to it so nothing changes under you, or use `latest` to always get the newest.
+That is the whole install. You do not need to download the source or build anything. The `0.6.11` is the version; you can pin to it so nothing changes under you, or use `latest` to always get the newest.
 
 (If you would rather build it yourself from source, you can, but you do not need to.)
 
@@ -136,7 +136,7 @@ Create a file called `docker-compose.yml` on your server (put it wherever you ke
 ```yaml
 services:
   alembic:
-    image: git.kretzer.club/andrew/alembic:0.6.9
+    image: git.kretzer.club/andrew/alembic:0.6.11
     container_name: alembic
     ports:
       - "8420:8420"

app/services/dedup_review_service.py

@@ -27,6 +27,38 @@ def _script_for_pass(pass_name: str) -> str:
     return _FUZZY_SCRIPT if pass_name == _FUZZY_PASS else _SCRIPT
 
 
+def _prune_stale_pending(db) -> int:
+    """Mark pending candidates whose delete_path or keep_path no longer
+    exists as resolved, instead of leaving them to surface forever.
+
+    A pending row can go stale without ever being confirmed through the UI --
+    e.g. a later scan's numbered-twin/format-upgrade auto-apply already
+    removed one side, or upgrade-mp3-to-flac replaced it, or someone deleted
+    it by hand. confirm_and_apply() already does this "already_gone" check
+    for candidates a user explicitly acts on; this generalizes it to run at
+    the start of every scan, so the pending list reflects current reality
+    instead of stale groups that something else already resolved."""
+    now = time.time()
+    rows = db.execute(
+        select(DedupCandidate).where(
+            DedupCandidate.applied == False,  # noqa: E712
+            DedupCandidate.confirmed == False,  # noqa: E712
+            DedupCandidate.ignored == False,  # noqa: E712
+        )
+    ).scalars().all()
+    pruned = 0
+    for c in rows:
+        if not Path(c.delete_path).exists() or not Path(c.keep_path).exists():
+            c.confirmed = True
+            c.confirmed_by = "auto:stale"
+            c.confirmed_at = now
+            c.applied = True
+            pruned += 1
+    if pruned:
+        db.commit()
+    return pruned
+
+
 def _is_pair_ignored(db, path_a: str, path_b: str) -> bool:
     """True if this path pair was ever marked 'keep both', regardless of
     which path was on the keep/delete side that time -- a later scan can
@@ -58,7 +90,9 @@ def _is_pair_already_pending(db, keep_path: str, delete_path: str) -> bool:
     return db.execute(query).first() is not None
 
 
-async def _run_scan(job_key: str, script_name: str, triggered_by: str) -> DedupRun | None:
+async def _run_scan(
+    job_key: str, script_name: str, triggered_by: str, extra_args: tuple[str, ...] = ()
+) -> DedupRun | None:
     """Returns None (persisting nothing) if the job never actually ran --
     e.g. skipped_lock because something else was using the pipeline lock
     at that moment. Same lesson as genre_review_service.run(): recording a
@@ -67,7 +101,7 @@ async def _run_scan(job_key: str, script_name: str, triggered_by: str) -> DedupR
     pending-candidates list isn't scoped to "latest run only"."""
     script = str(settings.pipeline_dir / "lib" / script_name)
     job_run, output = await pipeline_runner.run_job_capture(
-        job_key, [script, "--json"], triggered_by=triggered_by, timeout=_JOB_TIMEOUT_SECONDS
+        job_key, [script, "--json", *extra_args], triggered_by=triggered_by, timeout=_JOB_TIMEOUT_SECONDS
     )
     if job_run.status != "success":
         return None
@@ -76,6 +110,8 @@ async def _run_scan(job_key: str, script_name: str, triggered_by: str) -> DedupR
 
     db = SessionLocal()
     try:
+        _prune_stale_pending(db)
+        now = time.time()
         dedup_run = DedupRun(
             started_at=job_run.started_at,
             finished_at=job_run.finished_at,
@@ -91,7 +127,30 @@ async def _run_scan(job_key: str, script_name: str, triggered_by: str) -> DedupR
 
         skipped_ignored = 0
         skipped_duplicate = 0
+        auto_applied = 0
         for c in candidates:
+            if c.get("auto_applied"):
+                # dedup-library.sh already deleted this pair unconditionally
+                # (identical numbered-sibling twin: same dir/name/ext, no
+                # tag/fuzzy ambiguity involved) -- record it pre-applied for
+                # audit history; it never shows up as a pending review item.
+                db.add(
+                    DedupCandidate(
+                        dedup_run_id=dedup_run.id,
+                        pass_name=c.get("pass", "unknown"),
+                        keep_path=c["keep_path"],
+                        delete_path=c["delete_path"],
+                        delete_id=c.get("delete_id"),
+                        delete_size_bytes=c.get("delete_size_bytes"),
+                        confirmed=True,
+                        confirmed_by="auto:numbered_twin",
+                        confirmed_at=now,
+                        applied=True,
+                    )
+                )
+                auto_applied += 1
+                db.flush()
+                continue
             if _is_pair_ignored(db, c["keep_path"], c["delete_path"]):
                 skipped_ignored += 1
                 continue
@@ -116,8 +175,11 @@ async def _run_scan(job_key: str, script_name: str, triggered_by: str) -> DedupR
         db.commit()
         db.refresh(dedup_run)
         skipped_total = skipped_ignored + skipped_duplicate
+        if skipped_total or auto_applied:
             if skipped_total:
                 dedup_run.kept = (dedup_run.kept or 0) + skipped_total
+            if auto_applied:
+                dedup_run.deleted = auto_applied
             db.commit()
             db.refresh(dedup_run)
         return dedup_run
@@ -126,12 +188,23 @@ async def _run_scan(job_key: str, script_name: str, triggered_by: str) -> DedupR
 
 
 async def scan(triggered_by: str = "manual") -> DedupRun | None:
-    """Dry-run dedup-library.sh --json, persist every candidate deletion
+    """Dry-run dedup-library.sh --json (plus --auto-apply-numbered), persist
-    into a fresh dedup_runs/dedup_candidates pair. Never deletes anything
+    every candidate deletion into a fresh dedup_runs/dedup_candidates pair.
-    -- the scheduled maintenance:dedup job also only ever calls this (no
+
-    --apply), matching the false-negative-biased dedup preference; actual
+    Two kinds of match need no human judgment and get deleted unconditionally
-    deletion only ever happens through confirm_and_apply() below."""
+    by dedup-library.sh itself (see is_numbered_twin/is_format_upgrade there):
-    return await _run_scan("dedup:scan", _SCRIPT, triggered_by)
+    identical numbered-sibling twins (same dir, same name, same extension,
+    differing only by the ".N" collision suffix), and format upgrades within
+    an EXACT tag match from Pass 2/3 (case-insensitive/normalized already
+    proved same song via identical tags, so a differing extension there is
+    just "better format vs. worse"). Everything else -- including Pass 4's
+    cross-album fuzzy matches, where a wrong auto-delete could take out a
+    genuinely different version (a different album pressing, a DJ-mix edit,
+    etc.) -- stays a dry-run candidate awaiting manual confirm_and_apply()
+    below; that's the false-negative-biased preference for anything with real
+    ambiguity. Auto-applied deletions are reported here already applied,
+    purely for audit visibility."""
+    return await _run_scan("dedup:scan", _SCRIPT, triggered_by, extra_args=("--auto-apply-numbered",))
 
 
 async def scan_fuzzy(triggered_by: str = "manual") -> DedupRun | None:

pipeline/lib/dedup-library.sh

@@ -34,11 +34,26 @@ set -euo pipefail
 APPLY=0
 JSON_MODE=0
 ONLY_PATHS_FILE=""
+AUTO_APPLY_NUMBERED=0
 while [[ $# -gt 0 ]]; do
   case "$1" in
     --apply) APPLY=1; shift ;;
     --json) JSON_MODE=1; shift ;;
     --only-paths) ONLY_PATHS_FILE="$2"; shift 2 ;;
+    # Delete two kinds of match unconditionally, independent of
+    # --apply/--only-paths, while everything else stays dry-run/log-only:
+    #   - numbered-sibling twins (see is_numbered_twin): same dir, same name,
+    #     same extension, just the ".N" collision suffix -- the same download
+    #     landing twice.
+    #   - format upgrades within an exact tag match (see is_format_upgrade):
+    #     Pass 2/3 already proved same song via identical tags; a different
+    #     extension there just means "better format vs. worse", never a
+    #     different version.
+    # Excludes Pass 4 (cross-album fuzzy) entirely -- matching across
+    # different albums/directories is exactly where a different master or
+    # DJ-mix edit can share tags without being interchangeable, so it always
+    # needs a human. See dedup_review_service.scan().
+    --auto-apply-numbered) AUTO_APPLY_NUMBERED=1; shift ;;
     *) shift ;;
   esac
 done
@@ -97,6 +112,44 @@ host_path() {
 
 SEP=$'\x1c'  # ASCII file separator — safe with any music metadata
 
+# True if two paths are the SAME directory, SAME extension, and identical
+# basenames except for a numeric ".N" infix sldl/beets inserts on a filename
+# collision (e.g. "Title.flac" vs "Title.1.flac"). This is deliberately
+# narrower than any tag-based pass: no fuzzy matching, no cross-album
+# ambiguity, just the literal same download landing twice. Used to
+# auto-delete regardless of which pass found the pair -- Pass 1 only fires
+# when the canonical name is a beets ghost; the very common case where BOTH
+# copies are already tracked in beets (so Pass 1 defers) surfaces instead via
+# Pass 2/3's tag-based grouping, and still deserves the same free pass.
+is_numbered_twin() {
+  local a="$1" b="$2"
+  [[ "${a%/*}" == "${b%/*}" ]] || return 1
+  local ba="${a##*/}" bb="${b##*/}"
+  local ext="${ba##*.}"
+  [[ "${ext,,}" == "${bb##*.}" ]] || return 1
+  [[ "$(echo "$ba" | sed -E "s/\.[0-9]+\.${ext}\$/.${ext}/")" \
+     == "$(echo "$bb" | sed -E "s/\.[0-9]+\.${ext}\$/.${ext}/")" ]]
+}
+
+# True if this pair is a same-song format upgrade found by an EXACT tag match
+# (Pass 2 case-insensitive or Pass 3 normalized -- both require identical
+# albumartist+album+title after case/punctuation folding, so "same song" is
+# already proven by the pass itself) where the two files simply have
+# different extensions. rank_file() always ranks FLAC ahead of any other
+# format regardless of size/dirty-name/etc, so within a tag-exact group a
+# cross-extension pair unconditionally means "the format-preferred copy vs.
+# a lesser one" -- no judgment call. Deliberately excludes Pass 4
+# (cross_album_fuzzy): that pass matches by artist+title-base ACROSS
+# different albums/directories, which is exactly where a different master,
+# DJ-mix edit, or reissue can share tags without being an interchangeable
+# copy -- those still need a human to look at album/context before deleting
+# either side.
+is_format_upgrade() {
+  local pass="$1" keep="$2" delete="$3"
+  [[ "$pass" == "case_insensitive" || "$pass" == "normalized" ]] || return 1
+  [[ "${keep##*.}" != "${delete##*.}" ]]
+}
+
 # Rank a file: lower = better. FLAC > MP3 > other (WAV/etc.); clean filename
 # > sync-conflict artifact (-DESKTOP-, (1), .1.); extended/club mix > radio
 # edit at same format; then larger wins.
@@ -177,7 +230,7 @@ process_group() {
   esac
 
   local first=1
-  local keep_path=""
+  local keep_path="" keep_id="" any_auto=0
   while IFS="$SEP" read -r _sk id hp; do
     [[ -z "$hp" ]] && continue
     local size_bytes; size_bytes=$(stat -c '%s' "$hp" 2>/dev/null || echo 0)
@@ -185,14 +238,31 @@ process_group() {
     if [[ $first -eq 1 ]]; then
       log "  KEEP   ($size_h) $hp"
       keep_path="$hp"
+      keep_id="$id"
       first=0
     else
       log "  DELETE ($size_h) $hp"
-      json_emit "{\"pass\":\"${pass_name}\",\"keep_path\":\"$(json_escape "$keep_path")\",\"delete_path\":\"$(json_escape "$hp")\",\"delete_size_bytes\":${size_bytes}}"
+
+      # Auto-apply-numbered deletes numbered_sibling matches unconditionally,
+      # bypassing --only-paths (that gate exists only for the manual confirm
+      # flow, which never runs alongside this flag). All other passes stay
+      # dry-run/log-only here regardless.
+      local do_delete=0 auto_applied=0
       if [[ $APPLY -eq 1 ]]; then
+        do_delete=1
+      elif [[ $AUTO_APPLY_NUMBERED -eq 1 ]] \
+        && { is_numbered_twin "$keep_path" "$hp" || is_format_upgrade "$pass_name" "$keep_path" "$hp"; }; then
+        do_delete=1
+        auto_applied=1
+        any_auto=1
+      fi
+      local auto_json="false"; [[ $auto_applied -eq 1 ]] && auto_json="true"
+      json_emit "{\"pass\":\"${pass_name}\",\"keep_path\":\"$(json_escape "$keep_path")\",\"delete_path\":\"$(json_escape "$hp")\",\"delete_size_bytes\":${size_bytes},\"auto_applied\":${auto_json}}"
+
+      if [[ $do_delete -eq 1 ]]; then
         # With --only-paths given, only delete entries the caller explicitly
         # confirmed; without it, delete everything (original behavior).
-        if [[ -n "$ONLY_PATHS_FILE" && -z "${ONLY_PATHS[$hp]:-}" ]]; then
+        if [[ $auto_applied -eq 0 && -n "$ONLY_PATHS_FILE" && -z "${ONLY_PATHS[$hp]:-}" ]]; then
           log "    (skipped — not in --only-paths confirm list)"
         elif [[ -n "$id" ]]; then
           # In beets — beet remove -d removes from DB + disk. Best-effort: a
@@ -206,6 +276,18 @@ process_group() {
       fi
     fi
   done < <(echo "$ranked" | grep -v '^$' | sort -n)
+
+  # An auto-applied numbered-twin deletion can leave the numbered-named file
+  # as the sole survivor (it won on size despite the dirty-filename penalty).
+  # Rename it back to the canonical name so the library doesn't accumulate
+  # ".1."/".2." filenames for tracks that no longer have a duplicate. Only
+  # auto_applied triggers this (never a manual --only-paths confirm, which
+  # may leave the sibling undeleted if the user didn't confirm it -- renaming
+  # then would collide); only when it's actually in beets (a ghost survivor
+  # has nothing to move); only when the name still has the dirty infix.
+  if [[ $any_auto -eq 1 && -n "$keep_id" && "$keep_path" =~ \.[0-9]+\.[A-Za-z0-9]+$ ]]; then
+    beet move "id:${keep_id}" >> "$LOG" 2>&1 || log "    WARN: beet move id:${keep_id} failed (rename survivor)"
+  fi
   return 0  # explicit: the loop's last command status must not leak out under set -e
 }
 
@@ -248,16 +330,20 @@ while IFS="$SEP" read -r numbered_id numbered_cp; do
     # Canonical wins: delete numbered (in beets), keep canonical (ghost)
     process_group "P1 numbered-sibling: ${numbered_cp##*/Library/}" \
       "$host_canonical" "${numbered_id}${SEP}${numbered_cp}"
-    if [[ $APPLY -eq 1 ]]; then
+    if [[ $APPLY -eq 1 || $AUTO_APPLY_NUMBERED -eq 1 ]]; then
       # canonical is now a ghost file; import it into beets
       beet import -q -s "${canonical_cp}" >> "$LOG" 2>&1 || log "  WARN: beet import failed for ${canonical_cp}"
     fi
   else
     # Numbered wins (canonical is ghost): rm the ghost, then beet move to rename
     # the numbered file to the canonical path (id query — see process_group).
+    # Safe to reach with just AUTO_APPLY_NUMBERED: this loop only ever builds
+    # genuine numbered-sibling pairs (see is_numbered_twin), and process_group
+    # above already deleted the ghost canonical before this runs, so the move
+    # target is guaranteed clear -- no rename collision.
     process_group "P1 numbered-sibling: ${numbered_cp##*/Library/}" \
       "${numbered_id}${SEP}${numbered_cp}" "$host_canonical"
-    if [[ $APPLY -eq 1 ]]; then
+    if [[ $APPLY -eq 1 || $AUTO_APPLY_NUMBERED -eq 1 ]]; then
       beet move "id:${numbered_id}" >> "$LOG" 2>&1 || log "  WARN: beet move id:${numbered_id} failed"
     fi
   fi