diff --git a/data/README.md b/data/README.md
index 2988eabb1..49962b57f 100644
--- a/data/README.md
+++ b/data/README.md
@@ -6,14 +6,16 @@ All examples are run from the repository root and write their outputs under `tmp
 
 ## Per-command configs
 
-A per-command config is exactly the command's argument object. Every key has a matching `--flag`, and an explicit flag on the command line still overrides the file (flag > config > default).
+A per-command config is exactly the command's argument object. Its keys map one-to-one to the CLI flags: `--alignment a.fasta` is `alignment: [a.fasta]`, `--clock-rate 0.003` is `clock_rate: 0.003`, `--output-all dir` is `output_all: dir`. An explicit flag on the command line still overrides the file (flag > config > default).
 
 | File                                                                     | Command     | Demonstrates                                                |
 | ------------------------------------------------------------------------ | ----------- | ----------------------------------------------------------- |
 | [`ebola/20/ancestral-parsimony.yaml`](ebola/20/ancestral-parsimony.yaml) | `ancestral` | Fitch parsimony: fast, model-free ancestral states          |
 | [`zika/20/ancestral.yaml`](zika/20/ancestral.yaml)                       | `ancestral` | Marginal reconstruction with an inferred GTR model          |
+| [`sc2/2844/ancestral.yaml`](sc2/2844/ancestral.yaml)                     | `ancestral` | Marginal reconstruction on 2844 SARS-CoV-2 genomes          |
 | [`dengue/100/clock.yaml`](dengue/100/clock.yaml)                         | `clock`     | Root-to-tip regression with a non-default id column         |
 | [`flu/h3n2/20/optimize.yaml`](flu/h3n2/20/optimize.yaml)                 | `optimize`  | Branch-length optimization and min-divergence rerooting     |
+| [`mpox/clade-ii/1000/optimize.yaml`](mpox/clade-ii/1000/optimize.yaml)   | `optimize`  | The mpox `augur refine` replacement (mutations, no indels)  |
 | [`rsv/a/100/prune.yaml`](rsv/a/100/prune.yaml)                           | `prune`     | Dropping short, empty, and shared-mutation branches         |
 | [`zika/20/mugration.yaml`](zika/20/mugration.yaml)                       | `mugration` | Discrete ancestral geography over sampling country          |
 | [`flu/h3n2/200/timetree.yaml`](flu/h3n2/200/timetree.yaml)               | `timetree`  | Dated tree with a fixed clock rate and confidence intervals |
@@ -28,12 +30,14 @@ treetime ancestral --config data/zika/20/ancestral.yaml
 
 A pipeline file lists named steps, each an analysis command with its arguments. Steps run sequentially in one process. A step reads an earlier step's output with `{{ steps.<name>.outputs.<selection> }}`, so intermediate paths are never hand-written. `vars` names shared values once; a top-level `output_all` gives each step its own `<dir>/<step>/` output directory.
 
-| File                                                               | Chain                                   | Demonstrates                                       |
-| ------------------------------------------------------------------ | --------------------------------------- | -------------------------------------------------- |
-| [`mpox/clade-ii/20/pipeline.yaml`](mpox/clade-ii/20/pipeline.yaml) | `optimize` -> `ancestral`               | A Nextstrain-style mpox build in one file          |
-| [`zika/20/pipeline.yaml`](zika/20/pipeline.yaml)                   | `timetree` -> `mugration`               | Phylodynamics and phylogeography end to end        |
-| [`ebola/362/pipeline.yaml`](ebola/362/pipeline.yaml)               | `optimize` -> `ancestral` -> `timetree` | A full three-step build on a real epidemic dataset |
-| [`flu/h3n2/200/pipeline.yaml`](flu/h3n2/200/pipeline.yaml)         | `optimize` -> `timetree`                | A shared, typed clock rate defined once in `vars`  |
+| File                                                                   | Chain                                   | Demonstrates                                                     |
+| ---------------------------------------------------------------------- | --------------------------------------- | ---------------------------------------------------------------- |
+| [`zika/20/pipeline.yaml`](zika/20/pipeline.yaml)                       | `timetree` -> `mugration`               | Phylodynamics and phylogeography end to end                      |
+| [`flu/h3n2/200/pipeline.yaml`](flu/h3n2/200/pipeline.yaml)             | `optimize` -> `timetree`                | A shared, typed clock rate defined once in `vars`                |
+| [`flu/h3n2/500/pipeline.yaml`](flu/h3n2/500/pipeline.yaml)             | `optimize` -> `ancestral` -> `timetree` | A seasonal-influenza build with a fixed clock (500 sequences)    |
+| [`ebola/362/pipeline.yaml`](ebola/362/pipeline.yaml)                   | `optimize` -> `ancestral` -> `timetree` | A three-step build on the 2014 Ebola epidemic dataset            |
+| [`sc2/2844/pipeline.yaml`](sc2/2844/pipeline.yaml)                     | `optimize` -> `ancestral`               | A date-free build on 2844 SARS-CoV-2 genomes                     |
+| [`mpox/clade-ii/1000/pipeline.yaml`](mpox/clade-ii/1000/pipeline.yaml) | `optimize` -> `ancestral` -> `timetree` | The full Nextstrain mpox TreeTime chain (fixed clock, mutations) |
 
 Run a pipeline, preview its plan, or run only part of it:
 
@@ -60,7 +64,7 @@ treetime pipeline --config data/zika/20/pipeline.yaml --steps mugration
 - Validation is static and typed. `--check` and the JSON-schema-backed argument objects catch a bad parameter or a dangling step reference before anything runs; a Snakemake rule only surfaces a bad TreeTime parameter when that rule executes.
 - Reproducible and portable. The config is the exact serialized argument shape, with one dependency, committed beside the data.
 
-This is not a replacement for a full multi-sample workflow manager: incremental rebuilds, cluster scheduling, and non-TreeTime rules (subsampling, alignment, tree building, export) still belong to Snakemake and Augur. The pipeline replaces the TreeTime glue inside such a build. On the Nextstrain mpox `WIP/new_tt` phylogenetic workflow, for instance, `treetime optimize` replaces `augur refine` (branch-length optimization) and `treetime ancestral` folds in `augur translate`; the [`mpox/clade-ii/20/pipeline.yaml`](mpox/clade-ii/20/pipeline.yaml) example runs exactly that pair as one step chain.
+This is not a replacement for a full multi-sample workflow manager: incremental rebuilds, cluster scheduling, and non-TreeTime rules (subsampling, alignment, tree building, export) still belong to Snakemake and Augur. The pipeline replaces the TreeTime glue inside such a build. On the Nextstrain mpox `WIP/new_tt` phylogenetic workflow, for instance, three Snakemake rules drive TreeTime: `treetime optimize` replaces `augur refine` (branch-length optimization), `treetime ancestral` folds in `augur translate`, and `treetime timetree` dates the tree. The [`mpox/clade-ii/1000/pipeline.yaml`](mpox/clade-ii/1000/pipeline.yaml) example runs that chain as three steps in one file.
 
 ## Editor support
 
diff --git a/data/dengue/100/clock.yaml b/data/dengue/100/clock.yaml
index 4edfe3b17..7d40fabd1 100644
--- a/data/dengue/100/clock.yaml
+++ b/data/dengue/100/clock.yaml
@@ -10,9 +10,7 @@
 
 tree: "data/dengue/100/tree.nwk"
 metadata: "data/dengue/100/metadata.tsv"
-metadata_id:
-  metadata_id_columns:
-    - "genbank_accession"
+metadata_id_columns:
+  - "genbank_accession"
 
-output:
-  output_all: "tmp/examples/dengue/100/clock"
+output_all: "tmp/examples/dengue/100/clock"
diff --git a/data/ebola/20/ancestral-parsimony.yaml b/data/ebola/20/ancestral-parsimony.yaml
index 06bd150db..0f5211fcc 100644
--- a/data/ebola/20/ancestral-parsimony.yaml
+++ b/data/ebola/20/ancestral-parsimony.yaml
@@ -9,11 +9,9 @@
 
 tree: "data/ebola/20/tree.nwk"
 alignment:
-  alignment:
-    - "data/ebola/20/aln.fasta.xz"
+  - "data/ebola/20/aln.fasta.xz"
 
 # Fitch parsimony: fast, model-free ancestral states and mutations.
 method_anc: "parsimony"
 
-output:
-  output_all: "tmp/examples/ebola/20/ancestral-parsimony"
+output_all: "tmp/examples/ebola/20/ancestral-parsimony"
diff --git a/data/ebola/362/pipeline.yaml b/data/ebola/362/pipeline.yaml
index a62913cdf..389bd3cf4 100644
--- a/data/ebola/362/pipeline.yaml
+++ b/data/ebola/362/pipeline.yaml
@@ -23,8 +23,7 @@ steps:
     optimize:
       tree: "{{ vars.data }}/tree.nwk"
       alignment:
-        alignment:
-          - "{{ vars.data }}/aln.fasta.xz"
+        - "{{ vars.data }}/aln.fasta.xz"
       reroot: "min-dev"
 
   # 2. Reconstruct ancestral sequences and mutations on the optimized tree.
@@ -32,8 +31,7 @@ steps:
     ancestral:
       tree: "{{ steps.optimize.outputs.nwk }}"
       alignment:
-        alignment:
-          - "{{ vars.data }}/aln.fasta.xz"
+        - "{{ vars.data }}/aln.fasta.xz"
       method_anc: "marginal"
 
   # 3. Date the optimized tree, keeping the branch lengths from step 1.
@@ -42,7 +40,6 @@ steps:
       tree: "{{ steps.optimize.outputs.nwk }}"
       metadata: "{{ vars.data }}/metadata.tsv"
       alignment:
-        alignment:
-          - "{{ vars.data }}/aln.fasta.xz"
+        - "{{ vars.data }}/aln.fasta.xz"
       coalescent_opt: true
       max_iter: 3
diff --git a/data/flu/h3n2/20/optimize.yaml b/data/flu/h3n2/20/optimize.yaml
index 8ec9359c1..0e41fca03 100644
--- a/data/flu/h3n2/20/optimize.yaml
+++ b/data/flu/h3n2/20/optimize.yaml
@@ -9,11 +9,7 @@
 
 tree: "data/flu/h3n2/20/tree.nwk"
 alignment:
-  alignment:
-    - "data/flu/h3n2/20/aln.fasta.xz"
-
-model_args:
-  model: "infer"
+  - "data/flu/h3n2/20/aln.fasta.xz"
 
 # Per-edge optimizer: Brent's method in sqrt(t) space (the default, matches v0).
 opt_method: "brent-sqrt"
@@ -21,5 +17,4 @@ opt_method: "brent-sqrt"
 # Reroot by minimizing root-to-tip divergence variance (a date-free method).
 reroot: "min-dev"
 
-output:
-  output_all: "tmp/examples/flu/h3n2/20/optimize"
+output_all: "tmp/examples/flu/h3n2/20/optimize"
diff --git a/data/flu/h3n2/200/pipeline.yaml b/data/flu/h3n2/200/pipeline.yaml
index 69082c8a5..4b9e78e10 100644
--- a/data/flu/h3n2/200/pipeline.yaml
+++ b/data/flu/h3n2/200/pipeline.yaml
@@ -16,15 +16,12 @@ vars:
 output_all: "tmp/examples/flu/h3n2/200/pipeline"
 
 steps:
-  # Optimize branch lengths under an inferred GTR model.
+  # Optimize branch lengths under an inferred GTR model (the default).
   - name: "optimize"
     optimize:
       tree: "{{ vars.data }}/tree.nwk"
       alignment:
-        alignment:
-          - "{{ vars.data }}/aln.fasta.xz"
-      model_args:
-        model: "infer"
+        - "{{ vars.data }}/aln.fasta.xz"
 
   # Date the optimized tree with the fixed clock rate from `vars`.
   - name: "timetree"
@@ -32,8 +29,7 @@ steps:
       tree: "{{ steps.optimize.outputs.nwk }}"
       metadata: "{{ vars.data }}/metadata.tsv"
       alignment:
-        alignment:
-          - "{{ vars.data }}/aln.fasta.xz"
+        - "{{ vars.data }}/aln.fasta.xz"
       clock_rate: "{{ vars.clock_rate }}"
       clock_std_dev: "{{ vars.clock_std_dev }}"
       confidence: true
diff --git a/data/flu/h3n2/200/timetree.yaml b/data/flu/h3n2/200/timetree.yaml
index 167a6f82e..57b5176e4 100644
--- a/data/flu/h3n2/200/timetree.yaml
+++ b/data/flu/h3n2/200/timetree.yaml
@@ -12,8 +12,7 @@
 tree: "data/flu/h3n2/200/tree.nwk"
 metadata: "data/flu/h3n2/200/metadata.tsv"
 alignment:
-  alignment:
-    - "data/flu/h3n2/200/aln.fasta.xz"
+  - "data/flu/h3n2/200/aln.fasta.xz"
 
 clock_rate: 0.003
 clock_std_dev: 0.0006
@@ -21,7 +20,6 @@ confidence: true
 coalescent_opt: true
 max_iter: 3
 
-output:
-  output_all: "tmp/examples/flu/h3n2/200/timetree"
+output_all: "tmp/examples/flu/h3n2/200/timetree"
 # Confidence intervals are written to their own TSV when a path is given.
 output_confidence_tsv: "tmp/examples/flu/h3n2/200/timetree/confidence.tsv"
diff --git a/data/flu/h3n2/500/pipeline.yaml b/data/flu/h3n2/500/pipeline.yaml
new file mode 100644
index 000000000..896146893
--- /dev/null
+++ b/data/flu/h3n2/500/pipeline.yaml
@@ -0,0 +1,49 @@
+# Seasonal influenza H3N2 build: optimize, reconstruct, date (flu/h3n2/500).
+#
+# Run from the repository root:
+#   treetime pipeline --config data/flu/h3n2/500/pipeline.yaml
+#
+# Preview the plan, or resume from a later step after editing it:
+#   treetime pipeline --config data/flu/h3n2/500/pipeline.yaml --check
+#   treetime pipeline --config data/flu/h3n2/500/pipeline.yaml --steps timetree
+#
+# optimize -> ancestral -> timetree on 500 H3N2 hemagglutinin sequences. Seasonal
+# influenza has a well-characterized clock, so the rate is fixed
+# (`clock_rate` 0.003 substitutions/site/year) instead of estimated, defined once
+# in `vars` as a typed number. The optimized tree flows to the later steps through
+# `{{ steps.optimize.outputs.nwk }}`.
+
+vars:
+  data: "data/flu/h3n2/500"
+  clock_rate: 0.003
+  clock_std_dev: 0.0006
+
+output_all: "tmp/examples/flu/h3n2/500/pipeline"
+
+steps:
+  # Optimize branch lengths under an inferred GTR model.
+  - name: "optimize"
+    optimize:
+      tree: "{{ vars.data }}/tree.nwk"
+      alignment:
+        - "{{ vars.data }}/aln.fasta.xz"
+
+  # Reconstruct ancestral sequences and mutations on the optimized tree.
+  - name: "ancestral"
+    ancestral:
+      tree: "{{ steps.optimize.outputs.nwk }}"
+      alignment:
+        - "{{ vars.data }}/aln.fasta.xz"
+      method_anc: "marginal"
+
+  # Date the optimized tree with the fixed clock rate from `vars`.
+  - name: "timetree"
+    timetree:
+      tree: "{{ steps.optimize.outputs.nwk }}"
+      metadata: "{{ vars.data }}/metadata.tsv"
+      alignment:
+        - "{{ vars.data }}/aln.fasta.xz"
+      clock_rate: "{{ vars.clock_rate }}"
+      clock_std_dev: "{{ vars.clock_std_dev }}"
+      confidence: true
+      max_iter: 3
diff --git a/data/mpox/clade-ii/1000/optimize.yaml b/data/mpox/clade-ii/1000/optimize.yaml
new file mode 100644
index 000000000..a272f0c3b
--- /dev/null
+++ b/data/mpox/clade-ii/1000/optimize.yaml
@@ -0,0 +1,20 @@
+# Branch-length optimization for a Nextstrain mpox build (mpox/clade-ii/1000).
+#
+# Run from the repository root:
+#   treetime optimize --config data/mpox/clade-ii/1000/optimize.yaml
+#
+# This is the date-free step that replaces `augur refine` in the nextstrain/mpox
+# `WIP/new_tt` workflow. It re-estimates every branch length and reroots on the
+# minimum-divergence branch. mpox divergence is counted in absolute mutations
+# (`divergence_units: mutations`), and indels are excluded from the branch-length
+# likelihood (`no_indels`), matching the pipeline's `treetime optimize` rule.
+
+tree: "data/mpox/clade-ii/1000/tree.nwk"
+alignment:
+  - "data/mpox/clade-ii/1000/aln.fasta.xz"
+
+reroot: "min-dev"
+divergence_units: "mutations"
+no_indels: true
+
+output_all: "tmp/examples/mpox/clade-ii/1000/optimize"
diff --git a/data/mpox/clade-ii/1000/pipeline.yaml b/data/mpox/clade-ii/1000/pipeline.yaml
new file mode 100644
index 000000000..4da8cfd2a
--- /dev/null
+++ b/data/mpox/clade-ii/1000/pipeline.yaml
@@ -0,0 +1,65 @@
+# Nextstrain mpox build (clade IIb, hmpxv1), TreeTime part in one file (mpox/clade-ii/1000).
+#
+# Run from the repository root:
+#   treetime pipeline --config data/mpox/clade-ii/1000/pipeline.yaml
+#
+# Preview the whole plan, or resume after a failure, without recomputing earlier steps:
+#   treetime pipeline --config data/mpox/clade-ii/1000/pipeline.yaml --check
+#   treetime pipeline --config data/mpox/clade-ii/1000/pipeline.yaml --steps ancestral,timetree
+#
+# On the nextstrain/mpox `WIP/new_tt` phylogenetic workflow, three Snakemake
+# rules drive TreeTime: `treetime optimize` (replacing `augur refine`), then
+# `treetime ancestral` (folding in `augur translate`), then `treetime timetree`.
+# This file runs that same chain in one process.
+#
+# mpox is a slow-evolving DNA virus: divergence is measured in absolute mutations
+# (`divergence_units: mutations`), the clock rate is fixed rather than estimated
+# (`clock_rate` 5.7e-5 substitutions/site/year, with `clock_std_dev` for date
+# confidence), and indels are excluded from the branch-length likelihood
+# (`no_indels`). The clock constants live in `vars` as typed numbers, defined
+# once and reused. `{{ steps.optimize.outputs.nwk }}` carries the optimized tree
+# to the later steps with no hand-written path.
+
+vars:
+  data: "data/mpox/clade-ii/1000"
+  clock_rate: 5.7e-5
+  clock_std_dev: 2e-5
+
+output_all: "tmp/examples/mpox/clade-ii/1000/pipeline"
+
+steps:
+  # 1. Optimize branch lengths and reroot on the minimum-divergence branch.
+  - name: "optimize"
+    optimize:
+      tree: "{{ vars.data }}/tree.nwk"
+      alignment:
+        - "{{ vars.data }}/aln.fasta.xz"
+      reroot: "min-dev"
+      divergence_units: "mutations"
+      no_indels: true
+
+  # 2. Reconstruct ancestral sequences and mutations on the optimized tree.
+  - name: "ancestral"
+    ancestral:
+      tree: "{{ steps.optimize.outputs.nwk }}"
+      alignment:
+        - "{{ vars.data }}/aln.fasta.xz"
+      method_anc: "marginal"
+
+  # 3. Date the optimized tree with the fixed clock, keeping its root and polytomies.
+  - name: "timetree"
+    timetree:
+      tree: "{{ steps.optimize.outputs.nwk }}"
+      metadata: "{{ vars.data }}/metadata.tsv"
+      metadata_id_columns:
+        - "accession"
+      alignment:
+        - "{{ vars.data }}/aln.fasta.xz"
+      clock_rate: "{{ vars.clock_rate }}"
+      clock_std_dev: "{{ vars.clock_std_dev }}"
+      keep_root: true
+      keep_polytomies: true
+      divergence_units: "mutations"
+      no_indels: true
+      confidence: true
+      max_iter: 3
diff --git a/data/mpox/clade-ii/20/pipeline.yaml b/data/mpox/clade-ii/20/pipeline.yaml
deleted file mode 100644
index 3fdf81ac8..000000000
--- a/data/mpox/clade-ii/20/pipeline.yaml
+++ /dev/null
@@ -1,46 +0,0 @@
-# Nextstrain-style mpox build: branch-length optimization, then ancestral reconstruction.
-#
-# Run from the repository root:
-#   treetime pipeline --config data/mpox/clade-ii/20/pipeline.yaml
-#
-# Resolve the whole plan (inputs, outputs, chained paths) without running anything:
-#   treetime pipeline --config data/mpox/clade-ii/20/pipeline.yaml --check
-#
-# On the Nextstrain mpox `WIP/new_tt` phylogenetic workflow, `treetime optimize`
-# replaces `augur refine` (branch-length optimization only) and `treetime
-# ancestral` folds in `augur translate`. This one file runs both steps in one
-# process, on one dataset, with no snakemake, augur, or shell glue.
-#
-# `vars` names shared values once. `{{ steps.optimize.outputs.nwk }}` resolves
-# to the optimized tree the first step writes, so the second step never repeats
-# a path. `output_all` gives each step its own `<dir>/<step>/` output directory.
-
-vars:
-  data: "data/mpox/clade-ii/20"
-
-output_all: "tmp/examples/mpox/clade-ii/20/pipeline"
-
-steps:
-  # Re-estimate branch lengths and reroot on the min-divergence branch.
-  - name: "optimize"
-    optimize:
-      tree: "{{ vars.data }}/tree.nwk"
-      alignment:
-        alignment:
-          - "{{ vars.data }}/aln.fasta.xz"
-      model_args:
-        model: "infer"
-      reroot: "min-dev"
-      # mpox is measured in absolute substitutions rather than per-site rates.
-      divergence_units: "mutations"
-
-  # Reconstruct ancestral sequences and map mutations onto the optimized tree.
-  - name: "ancestral"
-    ancestral:
-      tree: "{{ steps.optimize.outputs.nwk }}"
-      alignment:
-        alignment:
-          - "{{ vars.data }}/aln.fasta.xz"
-      method_anc: "marginal"
-      model_args:
-        model: "infer"
diff --git a/data/rsv/a/100/prune.yaml b/data/rsv/a/100/prune.yaml
index 49c6071e8..dba102f3b 100644
--- a/data/rsv/a/100/prune.yaml
+++ b/data/rsv/a/100/prune.yaml
@@ -9,12 +9,10 @@
 
 tree: "data/rsv/a/100/tree.nwk"
 alignment:
-  alignment:
-    - "data/rsv/a/100/aln.fasta.xz"
+  - "data/rsv/a/100/aln.fasta.xz"
 
 prune_short: 1.0e-6
 prune_empty: true
 merge_shared_mutations: true
 
-output:
-  output_all: "tmp/examples/rsv/a/100/prune"
+output_all: "tmp/examples/rsv/a/100/prune"
diff --git a/data/sc2/2844/ancestral.yaml b/data/sc2/2844/ancestral.yaml
new file mode 100644
index 000000000..0732967c4
--- /dev/null
+++ b/data/sc2/2844/ancestral.yaml
@@ -0,0 +1,18 @@
+# Marginal ancestral reconstruction on 2844 SARS-CoV-2 genomes (sc2/2844).
+#
+# Run from the repository root:
+#   treetime ancestral --config data/sc2/2844/ancestral.yaml
+#
+# A large single-command run: marginal reconstruction treats every site
+# independently, fits a GTR rate matrix from the data (the default
+# `model: infer`), and maps nucleotide mutations onto the tree. The sparse
+# representation (the default) stores only variable sites, which keeps a
+# genome-length SARS-CoV-2 alignment tractable.
+
+tree: "data/sc2/2844/tree.nwk"
+alignment:
+  - "data/sc2/2844/aln.fasta.xz"
+
+method_anc: "marginal"
+
+output_all: "tmp/examples/sc2/2844/ancestral"
diff --git a/data/sc2/2844/pipeline.yaml b/data/sc2/2844/pipeline.yaml
new file mode 100644
index 000000000..9e6d855f5
--- /dev/null
+++ b/data/sc2/2844/pipeline.yaml
@@ -0,0 +1,35 @@
+# SARS-CoV-2 branch-length optimization and ancestral reconstruction (sc2/2844).
+#
+# Run from the repository root:
+#   treetime pipeline --config data/sc2/2844/pipeline.yaml
+#
+# Preview the plan without running anything:
+#   treetime pipeline --config data/sc2/2844/pipeline.yaml --check
+#
+# A date-free build on 2844 SARS-CoV-2 genomes: `optimize` re-estimates branch
+# lengths and reroots on the minimum-divergence branch, then `ancestral` maps
+# nucleotide mutations onto that tree. Neither step needs sampling dates, so this
+# runs on the tree and alignment alone. `{{ steps.optimize.outputs.nwk }}` passes
+# the optimized tree to the second step.
+
+vars:
+  data: "data/sc2/2844"
+
+output_all: "tmp/examples/sc2/2844/pipeline"
+
+steps:
+  # Re-estimate branch lengths under an inferred GTR model and reroot.
+  - name: "optimize"
+    optimize:
+      tree: "{{ vars.data }}/tree.nwk"
+      alignment:
+        - "{{ vars.data }}/aln.fasta.xz"
+      reroot: "min-dev"
+
+  # Reconstruct ancestral sequences and mutations on the optimized tree.
+  - name: "ancestral"
+    ancestral:
+      tree: "{{ steps.optimize.outputs.nwk }}"
+      alignment:
+        - "{{ vars.data }}/aln.fasta.xz"
+      method_anc: "marginal"
diff --git a/data/zika/20/ancestral.yaml b/data/zika/20/ancestral.yaml
index 4e339ae3f..19a303e39 100644
--- a/data/zika/20/ancestral.yaml
+++ b/data/zika/20/ancestral.yaml
@@ -4,17 +4,13 @@
 #   treetime ancestral --config data/zika/20/ancestral.yaml
 #
 # Marginal reconstruction treats every site independently and reports the
-# maximum-likelihood ancestral state per node. `--model infer` (the default)
-# fits a GTR rate matrix from the data and writes it alongside the tree.
+# maximum-likelihood ancestral state per node. It fits a GTR rate matrix from the
+# data (the default `model: infer`) and writes it alongside the tree.
 
 tree: "data/zika/20/tree.nwk"
 alignment:
-  alignment:
-    - "data/zika/20/aln.fasta.xz"
+  - "data/zika/20/aln.fasta.xz"
 
 method_anc: "marginal"
-model_args:
-  model: "infer"
 
-output:
-  output_all: "tmp/examples/zika/20/ancestral"
+output_all: "tmp/examples/zika/20/ancestral"
diff --git a/data/zika/20/mugration.yaml b/data/zika/20/mugration.yaml
index 26cded39a..1bbdcea3f 100644
--- a/data/zika/20/mugration.yaml
+++ b/data/zika/20/mugration.yaml
@@ -15,6 +15,5 @@ attribute: "country"
 weights: "data/zika/country_weights.csv"
 pc: 1.0
 
-output:
-  output_all: "tmp/examples/zika/20/mugration"
+output_all: "tmp/examples/zika/20/mugration"
 output_confidence_csv: "tmp/examples/zika/20/mugration/confidence.csv"
diff --git a/data/zika/20/pipeline.yaml b/data/zika/20/pipeline.yaml
index 4ecd33652..cdefc24db 100644
--- a/data/zika/20/pipeline.yaml
+++ b/data/zika/20/pipeline.yaml
@@ -25,8 +25,7 @@ steps:
       tree: "{{ vars.data }}/tree.nwk"
       metadata: "{{ vars.data }}/metadata.tsv"
       alignment:
-        alignment:
-          - "{{ vars.data }}/aln.fasta.xz"
+        - "{{ vars.data }}/aln.fasta.xz"
 
   # Reconstruct ancestral sampling country on the dated tree from step 1.
   - name: "mugration"
diff --git a/packages/app-cli/src/cli/pipeline/inputs.rs b/packages/app-cli/src/cli/pipeline/inputs.rs
index 1f1dc52e3..56bd36aa5 100644
--- a/packages/app-cli/src/cli/pipeline/inputs.rs
+++ b/packages/app-cli/src/cli/pipeline/inputs.rs
@@ -7,7 +7,7 @@ use serde_json::Value;
 /// disagree about what a step reads.
 pub const INPUT_FIELDS: [(&str, &[&str]); 5] = [
   ("tree", &["tree"]),
-  ("alignment", &["alignment", "alignment"]),
+  ("alignment", &["alignment"]),
   ("metadata", &["metadata"]),
   ("weights", &["weights"]),
   ("vcf-reference", &["vcf_reference"]),
diff --git a/packages/app-cli/src/cli/pipeline/resolve.rs b/packages/app-cli/src/cli/pipeline/resolve.rs
index 265ed8021..32fcc064d 100644
--- a/packages/app-cli/src/cli/pipeline/resolve.rs
+++ b/packages/app-cli/src/cli/pipeline/resolve.rs
@@ -302,18 +302,15 @@ fn resolve_selection_path(step: &str, producer: &ResolvedStep, selection: &str)
   }
 }
 
-/// Set `output.output_all` to `dir` unless the step already configured its own output directory.
+/// Set the top-level `output_all` to `dir` unless the step already configured its own output
+/// directory. `output_all` is a flattened field, so it sits at the top level of the step payload.
 fn set_output_all_if_absent(payload: &mut Value, dir: &Path) {
   let Value::Object(map) = payload else {
     return;
   };
-  let output = map.entry("output").or_insert_with(|| Value::Object(Map::new()));
-  let Value::Object(output) = output else {
-    return;
-  };
-  let already_set = matches!(output.get("output_all"), Some(value) if !value.is_null());
+  let already_set = matches!(map.get("output_all"), Some(value) if !value.is_null());
   if !already_set {
-    output.insert(
+    map.insert(
       "output_all".to_owned(),
       Value::String(dir.to_string_lossy().into_owned()),
     );
@@ -395,8 +392,8 @@ mod tests {
   fn test_resolve_chain_uses_explicit_step_output_all() {
     let config = json!({
       "steps": [
-        { "name": "tt", "timetree": { "tree": "in.nwk", "metadata": "m.tsv", "output": { "output_all": "out/tt" } } },
-        { "name": "anc", "ancestral": { "tree": "{{ steps.tt.outputs.nwk }}", "output": { "output_all": "out/anc" } } }
+        { "name": "tt", "timetree": { "tree": "in.nwk", "metadata": "m.tsv", "output_all": "out/tt" } },
+        { "name": "anc", "ancestral": { "tree": "{{ steps.tt.outputs.nwk }}", "output_all": "out/anc" } }
       ]
     });
     let resolved = resolve(config).unwrap();
@@ -409,7 +406,7 @@ mod tests {
     let config = json!({
       "output_all": "tmp/run",
       "steps": [
-        { "name": "tt", "timetree": { "tree": "in.nwk", "metadata": "m.tsv", "output": { "output_nwk_style": ["plain", "beast"] } } },
+        { "name": "tt", "timetree": { "tree": "in.nwk", "metadata": "m.tsv", "output_nwk_style": ["plain", "beast"] } },
         { "name": "anc", "ancestral": { "tree": "{{ steps.tt.outputs.nwk }}" } }
       ]
     });
diff --git a/packages/app-cli/src/cli/pipeline/safety.rs b/packages/app-cli/src/cli/pipeline/safety.rs
index 265385cc3..d46826244 100644
--- a/packages/app-cli/src/cli/pipeline/safety.rs
+++ b/packages/app-cli/src/cli/pipeline/safety.rs
@@ -141,8 +141,8 @@ mod tests {
   fn test_safety_output_collision_rejected() {
     let pipeline = resolve(json!({
       "steps": [
-        { "name": "a", "ancestral": { "tree": "in.nwk", "output": { "output_tree_nwk": "shared.nwk" } } },
-        { "name": "b", "ancestral": { "tree": "in.nwk", "output": { "output_tree_nwk": "shared.nwk" } } }
+        { "name": "a", "ancestral": { "tree": "in.nwk", "output_tree_nwk": "shared.nwk" } },
+        { "name": "b", "ancestral": { "tree": "in.nwk", "output_tree_nwk": "shared.nwk" } }
       ]
     }));
     let result = validate_plan(&pipeline, None);
@@ -157,7 +157,7 @@ mod tests {
   fn test_safety_self_truncation_rejected() {
     let pipeline = resolve(json!({
       "steps": [
-        { "name": "a", "ancestral": { "tree": "same.nwk", "output": { "output_tree_nwk": "same.nwk" } } }
+        { "name": "a", "ancestral": { "tree": "same.nwk", "output_tree_nwk": "same.nwk" } }
       ]
     }));
     let result = validate_plan(&pipeline, None);
diff --git a/packages/treetime/src/commands/ancestral/args.rs b/packages/treetime/src/commands/ancestral/args.rs
index ebe8378fc..6e9e80f86 100644
--- a/packages/treetime/src/commands/ancestral/args.rs
+++ b/packages/treetime/src/commands/ancestral/args.rs
@@ -26,6 +26,7 @@ pub struct TreetimeAncestralArgsRaw {
   pub config_args: ConfigArgs,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub alignment: AlignmentArgs,
 
   /// FASTA file of the sequence the VCF was mapped to (only for vcf input)
@@ -41,9 +42,11 @@ pub struct TreetimeAncestralArgsRaw {
   pub tree: Option<PathBuf>,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub alphabet_args: AlphabetArgs,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub model_args: ModelArgs,
 
   /// Method used for reconstructing ancestral sequences
@@ -58,6 +61,7 @@ pub struct TreetimeAncestralArgsRaw {
   pub dense: Option<bool>,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub gap_fill_args: GapFillArgs,
 
   /// Zero-based mutation indexing
@@ -161,6 +165,7 @@ pub struct TreetimeAncestralArgsRaw {
   pub output_reconstructed_aa_fasta: Option<String>,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub output: OutputCoreArgs,
 
   /// Comma-separated list of outputs to produce with `--output-all`.
@@ -175,6 +180,7 @@ pub struct TreetimeAncestralArgsRaw {
   pub output_selection: Vec<AncestralOutputSelection>,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub topology_order: TopologyOrderArgs,
 
   /// Number of outer GTR refinement iterations.
diff --git a/packages/treetime/src/commands/clock/args.rs b/packages/treetime/src/commands/clock/args.rs
index 771c49920..aadec44ad 100644
--- a/packages/treetime/src/commands/clock/args.rs
+++ b/packages/treetime/src/commands/clock/args.rs
@@ -27,6 +27,7 @@ pub struct TreetimeClockArgsRaw {
   pub config_args: ConfigArgs,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub alignment: AlignmentArgs,
 
   /// Name of file containing the tree in newick, nexus, or phylip format.
@@ -47,9 +48,11 @@ pub struct TreetimeClockArgsRaw {
   pub metadata: Option<PathBuf>,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub metadata_id: MetadataIdArgs,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub date_column: DateColumnArgs,
 
   /// Length of the sequence, used to calculate expected variation in branch length. Not required if alignment is provided.
@@ -57,6 +60,7 @@ pub struct TreetimeClockArgsRaw {
   pub sequence_length: Option<usize>,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub model_args: ModelArgs,
 
   /// If set to 'input', the provided branch length will be used without modification. Note that branch lengths optimized by treetime are only accurate at short evolutionary distances.
@@ -73,6 +77,7 @@ pub struct TreetimeClockArgsRaw {
   pub clock_filter: f64,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub reroot: RerootArgs,
 
   /// don't reroot the tree. Otherwise, reroot to minimize the residual of the regression of
@@ -97,6 +102,7 @@ pub struct TreetimeClockArgsRaw {
   pub allow_negative_rate: bool,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub output: OutputCoreArgs,
 
   /// Path to output clock model JSON.
@@ -123,6 +129,7 @@ pub struct TreetimeClockArgsRaw {
   pub output_selection: Vec<ClockOutputSelection>,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub topology_order: TopologyOrderArgs,
 
   /// Random seed
@@ -246,14 +253,17 @@ pub struct BranchSplitArgs {
 
   /// Grid search parameters
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub grid_params: GridSearchParams,
 
   /// Brent's method parameters
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub brent_params: BrentParams,
 
   /// Golden section search parameters
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub golden_params: GoldenSectionParams,
 }
 
@@ -264,5 +274,6 @@ pub struct BranchSplitArgs {
 pub struct ClockRegressionArgs {
   /// Clock regression model parameters
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub clock_params: ClockParams,
 }
diff --git a/packages/treetime/src/commands/mugration/args.rs b/packages/treetime/src/commands/mugration/args.rs
index 7fd03a3cd..ffb6e11e8 100644
--- a/packages/treetime/src/commands/mugration/args.rs
+++ b/packages/treetime/src/commands/mugration/args.rs
@@ -41,6 +41,7 @@ pub struct TreetimeMugrationArgsRaw {
   pub weights: Option<PathBuf>,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub metadata_id: MetadataIdArgs,
 
   /// Path to output state-probability-profile CSV.
@@ -118,6 +119,7 @@ pub struct TreetimeMugrationArgsRaw {
   pub seed: Option<u64>,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub output: OutputCoreArgs,
 
   /// Comma-separated list of outputs to produce with `--output-all`.
@@ -132,6 +134,7 @@ pub struct TreetimeMugrationArgsRaw {
   pub output_selection: Vec<MugrationOutputSelection>,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub topology_order: TopologyOrderArgs,
 }
 
diff --git a/packages/treetime/src/commands/optimize/args.rs b/packages/treetime/src/commands/optimize/args.rs
index d48d4573b..d460ca750 100644
--- a/packages/treetime/src/commands/optimize/args.rs
+++ b/packages/treetime/src/commands/optimize/args.rs
@@ -45,6 +45,7 @@ pub struct TreetimeOptimizeArgsRaw {
   pub config_args: ConfigArgs,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub alignment: AlignmentArgs,
 
   /// Name of file containing the tree in newick, nexus, or phylip format.
@@ -55,9 +56,11 @@ pub struct TreetimeOptimizeArgsRaw {
   pub tree: Option<PathBuf>,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub alphabet_args: AlphabetArgs,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub model_args: ModelArgs,
 
   /// Use dense representation of sequences on the tree
@@ -69,6 +72,7 @@ pub struct TreetimeOptimizeArgsRaw {
   pub dense: Option<bool>,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub output: OutputCoreArgs,
 
   /// Units for divergence values in augur node data JSON output.
@@ -107,6 +111,7 @@ pub struct TreetimeOptimizeArgsRaw {
   pub output_selection: Vec<OptimizeOutputSelection>,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub topology_order: TopologyOrderArgs,
 
   /// Maximum number of iterations
@@ -192,6 +197,7 @@ pub struct TreetimeOptimizeArgsRaw {
   pub keep_root: bool,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub gap_fill_args: GapFillArgs,
 }
 
diff --git a/packages/treetime/src/commands/prune/args.rs b/packages/treetime/src/commands/prune/args.rs
index 4888afc76..823df02e3 100644
--- a/packages/treetime/src/commands/prune/args.rs
+++ b/packages/treetime/src/commands/prune/args.rs
@@ -21,6 +21,7 @@ pub struct TreetimePruneArgsRaw {
   pub config_args: ConfigArgs,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub alignment: AlignmentArgs,
 
   /// Name of file containing the tree in newick, nexus, or phylip format.
@@ -29,9 +30,11 @@ pub struct TreetimePruneArgsRaw {
   pub tree: Option<PathBuf>,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub alphabet_args: AlphabetArgs,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub output: OutputCoreArgs,
 
   /// Path to output GTR model JSON.
@@ -52,6 +55,7 @@ pub struct TreetimePruneArgsRaw {
   pub output_selection: Vec<PruneOutputSelection>,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub topology_order: TopologyOrderArgs,
 
   /// Threshold value for pruning of branches
diff --git a/packages/treetime/src/commands/timetree/args.rs b/packages/treetime/src/commands/timetree/args.rs
index 9d87fca35..f99ff9f5c 100644
--- a/packages/treetime/src/commands/timetree/args.rs
+++ b/packages/treetime/src/commands/timetree/args.rs
@@ -37,6 +37,7 @@ pub struct TreetimeTimetreeArgsRaw {
   pub config_args: ConfigArgs,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub alignment: AlignmentArgs,
 
   /// Name of file containing the tree in newick, nexus, or phylip format.
@@ -57,9 +58,11 @@ pub struct TreetimeTimetreeArgsRaw {
   pub metadata: Option<PathBuf>,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub metadata_id: MetadataIdArgs,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub date_column_args: DateColumnArgs,
 
   /// Length of the sequence, used to calculate expected variation in branch length. Not required if alignment is provided.
@@ -213,6 +216,7 @@ pub struct TreetimeTimetreeArgsRaw {
   pub n_iqd: Option<f64>,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub reroot: RerootArgs,
 
   /// don't reroot the tree. Otherwise, reroot to minimize the residual of the regression of
@@ -234,6 +238,7 @@ pub struct TreetimeTimetreeArgsRaw {
   pub covariation: bool,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub model_args: ModelArgs,
 
   /// Method used for reconstructing ancestral sequences
@@ -241,6 +246,7 @@ pub struct TreetimeTimetreeArgsRaw {
   pub method_anc: MethodAncestral,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub alphabet_args: AlphabetArgs,
 
   /// Use dense representation for sequences (store full probability distributions)
@@ -248,6 +254,7 @@ pub struct TreetimeTimetreeArgsRaw {
   pub dense: Option<bool>,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub gap_fill_args: GapFillArgs,
 
   /// Zero-based mutation indexing
@@ -357,6 +364,7 @@ pub struct TreetimeTimetreeArgsRaw {
   pub output_coalescent_json: Option<PathBuf>,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub output: OutputCoreArgs,
 
   /// Comma-separated list of outputs to produce with `--output-all`.
@@ -371,6 +379,7 @@ pub struct TreetimeTimetreeArgsRaw {
   pub output_selection: Vec<TimetreeOutputSelection>,
 
   #[cfg_attr(feature = "clap", clap(flatten))]
+  #[serde(flatten)]
   pub topology_order: TopologyOrderArgs,
 
   /// Random seed