Add ALCARECO skims (KS, Lambda, D*, J/psi, Upsilon, Z) and persist resonance candidates

[davidwalter2]

Summary

Adds ALCARECO skims for the muon-momentum-scale calibration covering V0
(KS, Lambda), three-body (D*), dimuon (J/psi, Upsilon, Z) and J/psi+X
(B-meson / quarkonium) channels, and persists a
reco::VertexCompositeCandidateCollection per stream so downstream
consumers can iterate the candidates and follow daughter TrackRefs into
the cloned ALCAReco track collection without going back to generalTracks:

• TkAlKsToPiPi — V0 (KS → π⁺π⁻)
• TkAlLambdaToProtonPi — V0 (Λ → pπ⁻)
• TkAlDstToD0Pi — D*⁺ → D⁰(K⁻π⁺) πs⁺ (three-track topology with a soft-pion tag)
• TkAlJpsiMuMu, TkAlUpsilonMuMu, TkAlZMuMu — dimuon resonances (V0-pattern: candidate is built upstream by TwoBodyDecayCandidateProducer)
• TkAlJpsiX — 8 channels: B⁺ → J/ψK⁺, B⁰ → J/ψK*⁰, B⁰ → J/ψKs, Bs → J/ψφ, Λb → J/ψΛ, ψ(2S) → J/ψπ⁺π⁻, Bc⁺ → J/ψπ⁺, plus a J/ψ-only channel on a loose muon selection

Each skim stores the daughter tracks (cloned, with hits + clusters) and
publishes *Resonances candidate collections with daughter TrackRefs
into the cloned tracks. Selection cuts (mass window, charge, V0 Lxy /
cosθXY) are applied at the candidate-builder level.

What's in this PR

16 commits on top of 6e29f933a55, in three blocks:

Block 1 — V0 / D* / dimuon skims + resonance persistence (commits 1–6)

1. 0960cf87c4f — Infrastructure for TkAlDstToD0Pi (Elisabetta Manca): three-body decay selector module + ALCARECO cff + validation analyzer
2. 37b68d22f1f — Removes the validation analyzer (kept the selector)
3. 3149b4a77a1 — Removes HLT preselection so the ALCARECO is usable across triggers
4. 1d2bf1a7599 — Adds TkAlKsToPiPi + TkAlLambdaToProtonPi V0 skims via AlignmentTracksFromV0Selector
5. c932a392d9d — Replaces AlignmentTracksFromV0Selector with V0DaughterTrackProducer (extracts daughter tracks from a private ALCARECOTkAlV0Candidates collection — a clone of generalV0Candidates with a lower track-pT cut, leaving the standard reco V0 collection untouched). Adds optional per-track dE/dx ValueMap projection (strip / pixel / joint Harmonic-2) for downstream particle-ID.
6. df64a66c5fb — Persists the resonance-candidate collection for every stream and adds dimuon streams (J/psi, Upsilon, Z) on the V0 pattern.

Block 2 — output format (commit 7)

7. b8ebaa3d9f2 — Writes ALCARECO PoolOutputModules at ROOT split level 1 (alcarecoSplitLevel.py customise) so 10_6-produced files stay readable in CMSSW ≥ 15_0 (works around ROOT Replace boost with standard library equivalents cms-sw/cmssw#19773: v11→v14 SiStripCluster schema-evolution read rule not firing on fully-split branches).

Block 3 — TkAlJpsiX stream (commits 8–16, Pietro Lugato)

8. 4d65009c736 — registers TkAlJpsiX in central AlCa (autoAlca.py: Charmonium, MuOniaParked; AlCaRecoStreams_cff.py, AlCaRecoOutput_cff.py)
9. 86af90df597 — helix propagation of daughter tracks to a candidate-level common point + more TwoBodyDecayCandidateProducer options
10. 5952d2d08bb — BuildFile dependencies for the J/psi+X producers (KinematicFit, TransientTrack, …)
11. e20a850141f — CompositeDaughterTrackProducer: merged, deduplicated leaf-track collection across all channels
12. 04efb4538e5 — JpsiXCandidateProducer covering all 7 J/psi+X decay channels (track mode for B⁺/Bc, VCC mode for nested resonances)
13. c560219c6bf — TkAlJpsiX output module keep/drop list
14. 026705dd9ec — cff wiring of the 7 channels, V0 clone with reduced pT floor, per-channel remappers
15. 420fe8859d8 — persists muon info (ALCARECOTkAlJpsiXLooseMuons + AlignmentTrackToMuonAssociator track→muon association), adds the J/ψ-only channel on a loose muon ID, fixes the bachelor-eta cut, and rewires ψ(2S) to prompt π⁺π⁻ (was incorrectly sourced from the displaced V0 Ks output)
16. e77e7e0a5a6 — requires high-purity tracks (D*) and per-daughter pT thresholds

Commit 6 details

• TwoBodyDecayCandidateProducer: builds a VertexCompositeCandidateCollection from opposite-sign track pairs in a configurable mass window, with optional muon-ID prefilter via muonSrc. Replaces the in-AlignmentTrackSelector pair finding for the dimuon streams; daughters use V0Producer's positive-charge-first convention.
• AlignmentTrackSelectorWithIndexMapModule: drop-in replacement for AlignmentTrackSelectorModule that, alongside the standard cloned Track + TrackExtra + RecHit + Cluster outputs, emits an edm::ValueMap<unsigned int> (instance label originalIndex) of source-collection indices computed by pointer arithmetic on the selector chain's Track* output. No kinematic fingerprinting. Required because helper::TrackCollectionStoreManager::processTrack rewrites the cloned tracks' TrackExtraRefs to a fresh sequential key, destroying the link to generalTracks.
• VertexCompositeCandidateRemapper: rewrites each candidate's daughter TrackRefs to point at the cloned ALCAReco track collection via the originalIndex ValueMap chain (selH idx → intermediateTracks idx → intermediateTracks.extra().key() = generalTracks idx). Recurses into nested composites (e.g. for B → J/psi K).
• Bug fix in DeDxValueMapProjector: previously used selectedTrack.extra().key() as the source-track index, but after TrackCollectionStoreManager's clone-and-store that key is just the position in the new collection (0,1,2,…). The persisted dE/dx values for V0 / D* daughters were therefore values of unrelated generalTracks[j] entries. Switched to the same originalIndex chain.
• All six streams' cffs rewired to publish a *Resonances VertexCompositeCandidateCollection alongside the cloned-track output; the corresponding _Output_cff.py files keep the new products.
• Adds recoskim_Run2016G_SingleMuon_AllResonances.py covering all streams in a single test job; removes the older partial test configs (Dst, KsLambda, KsLambdaDst).

TkAlJpsiX details (block 3)

Five-stage single-sequence architecture (ALCARECOTkAlJpsiX_cff.py):
DCS filter + muon selectors → shared candidate construction (J/ψ, V0s, K*⁰, φ, π⁺π⁻) → 8 per-channel JpsiXCandidateProducer / TwoBodyDecayCandidateProducer instances → merged deduplicated leaf-track collection (CompositeDaughterTrackProducer) → AlignmentTrackSelectorWithIndexMap cloning + 3 dE/dx projectors → 8 per-channel VertexCompositeCandidateRemappers. The persisted output is a single deduplicated cloned-track collection + 8 remapped candidate collections + persisted loose muons + a track→muon edm::Association.

• JpsiXCandidateProducer: two modes — track (bachelor from generalTracks; B⁺, Bc) and vcc (second VertexCompositeCandidate; B⁰, Bs, Λb, ψ(2S)). Dimuon (and X-pair) 4-momenta are helix-propagated to their pair PCA before the mass calculation (removes an O(1–3 MeV) ctau-correlated bias at displaced vertices). Optional J/ψ mass constraint and B-level KinematicConstrainedVertexFitter fit with vertex-prob / pointing-angle / Lxy-significance cuts.
• Selection presets A / B / C (mass-windows-only / Phase-1-locked kinematic cuts / + B-level Kalman vertex fit) selected via the TKALJPSIX_SELECTION_PRESET env var at python-load time; default B.
• The shared ALCARECOTkAlV0Candidates clone loosens vertex-quality and IP-significance cuts (vtxChi2Cut 6.63→15, vtxDecaySigXYCut 15→10, cosThetaXYCut 0.998→0.995, tkIPSigXYCut 2→1) on top of the pT floor 0.35→0.1 GeV, for the alignment use case only.

New plugins

• Alignment/CommonAlignmentProducer/plugins/V0DaughterTrackProducer.cc — KS / Λ daughter extraction
• Alignment/CommonAlignmentProducer/src/AlignmentThreeBodyDecayTrackSelector.cc — D* daughter selection (used by the existing AlignmentTrackSelectorModule)
• Alignment/CommonAlignmentProducer/plugins/DeDxValueMapProjector.cc — per-track dE/dx ValueMap projector (ref-based via originalIndex)
• Alignment/CommonAlignmentProducer/plugins/TwoBodyDecayCandidateProducer.cc — two-track candidate builder (dimuon, K*⁰, φ, π⁺π⁻; asymmetric mass hypotheses, optional Kalman vertex fit, track-track DOCA cut)
• Alignment/CommonAlignmentProducer/plugins/AlignmentTrackSelectorWithIndexMapModule.cc — selector + originalIndex ValueMap
• Alignment/CommonAlignmentProducer/plugins/VertexCompositeCandidateRemapper.cc — candidate daughter-ref remapper
• Alignment/CommonAlignmentProducer/plugins/JpsiXCandidateProducer.cc — J/ψ+X mother-candidate builder (7 channels)
• Alignment/CommonAlignmentProducer/plugins/CompositeDaughterTrackProducer.cc — merged deduplicated leaf-track extraction from nested candidates
• Alignment/CommonAlignmentProducer/plugins/AlignmentTrackToMuonAssociator.cc — cloned-track → reco::Muon association

New cff/cfi

• ALCARECOTkAlV0Candidates_cff.py (private V0Producer clone, shared by V0 skims and TkAlJpsiX)
• ALCARECOTkAl{KsToPiPi,LambdaToProtonPi,DstToD0Pi,JpsiMuMu,UpsilonMuMu,ZMuMu,JpsiX}_cff.py + each _Output_cff.py
• alcaDedxJointEstimator_cfi.py
• AlignmentTrackSelectorWithIndexMap_cfi.py
• alcarecoSplitLevel.py (split-level-1 customise function)
• TkAlLooseIdMuonSelector added to TkAlMuonSelectors_cfi.py

Plus updates to BuildFile.xml, AlCaRecoOutput_cff.py, AlCaRecoStreams_cff.py, AlignmentTrackSelector_cfi.py (new ThreeBodyDecaySelector PSet), and autoAlca.py.

Test plan

• Build with scram b -j16 in CMSSW_10_6_17_patch1
• Run on 1 RAW file (1000 events SingleMuon Run2016G + 1 file Charmonium); verify all six streams produce expected outputs and edmDumpEventContent shows the new *_*Resonances_*_* candidate branches
• Verify candidate daughter TrackRefs resolve into the cloned ALCAReco track collection (100% id-match on the first candidate of every event across all streams)
• Verify dE/dx values are physical (mean ~2.8 MeV/cm, sd ~1, broad value uniqueness — confirms the originalIndex-chain bug fix)
• Larger production: 100 RAW Charmonium files (run 279654, ~50k events × 10 parallel jobs × 16 threads) — ~30 min wallclock
• Stage-2 CVH 9-variant scan (KS, Λ, J/psi × no-vtx/vtx/vtx+pointing) on the 100-file ALCAReco — 9/9 success, J/psi mass peaks at 3.093 ± 0.068 GeV
• Rebuild (scram b -j8) clean after merging the TkAlJpsiX commits (block 3)
• TkAlJpsiX stream validation on RAW data (block 3 — @pmlugato)

Review fixes applied (commit 444b20f2062)

• JpsiXCandidateProducer vcc mode: added the missing overlap veto between the J/ψ muon tracks and the X-candidate daughter tracks (track mode already had one via jpsiDaughterKeys). Previously a K*⁰/φ/π⁺π⁻ candidate reusing a J/ψ muon produced a duplicate-track mother candidate — the DOCA cut passed trivially (DOCA = 0) and, under preset C, the multi-track Kalman fit received the same track twice.
• Daughter pdgId signs: hadrons now carry the sign of the track charge (K⁺ = +321; previously tagged -321 by the lepton convention); leptons unchanged (μ⁻ = +13). Sign is derived from the actual track charge, so same-sign pairs are self-consistent. ⚠️ Any downstream tooling matching on signed pdgId needs a corresponding update; |pdgId| (mass hypothesis) is unchanged.
• VertexCompositeCandidateRemapper: remapped candidates now carry the source candidate's vertex covariance and fit χ²/ndof (previously dropped).
• TwoBodyDecayCandidateProducer: KalmanVertexFitter::vertex() exception-guarded (a VertexException drops the pair instead of killing the job); dormant since applyVertexFit=False everywhere, but safe if enabled.
• AlignmentThreeBodyDecayTrackSelector: end-of-job summary via MessageLogger instead of std::cout.
• Stale ψ(2S) "V0-mode" comments corrected in ALCARECOTkAlJpsiX_cff.py.

Open items from review

• The TKALJPSIX_SELECTION_PRESET env-var switch is convenient for private production but makes the cff non-reproducible from the config file alone; central AlCa integration would need it replaced by a cms.Parameter / customise function.
• The J/ψ-only loose-muon channel is gated by the tight-muon event filter (ALCARECOTkAlJpsiXGoodMuons, filter=True), so events whose muons are all loose-only are not captured.

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