Restructure: descriptive tier and experiment names, paper/manuscript

- paper/pnas -> paper/manuscript (venue-neutral)
- configs/layer1 -> configs/inheritance, src/knowledge -> src/inheritance
  (imported as `inheritance`), make layer1 -> make inheritance; layer2 alias dropped
- inheritance and trained-network bundles named after the manuscript figure
  they feed (fig2_grounding_sweep, figS3_rebaselining, ...), or descriptively
  where they feed none; configs keep their `experiment:` value so parquet
  hashes are unchanged, only output.dir moves
- figure scripts, SI figure sources, notebooks, REPRODUCING.md, README and the
  SI Methods/tables updated; make clean no longer deletes tracked manifests;
  reproduce.sh hashes the s{seed}/ layouts too

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Y64o8FKP7rCuXzC48pxpMm

results/figS5_aimed_grounding/README.md

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+# E3 — Grounding must overlap the content it protects
+
+**Claim tested:** if your budget of real data is fixed, does it matter *where* you spend it? Is it
+enough to sprinkle real data uniformly, or must it target the knowledge you care about?
+
+**Setup (Layer 1, pure math).** `K = 1000` items divided into `R = 10` disjoint **regions** (think
+subject areas). `n = 200`, 400 generations, 100 repeats. The **same total** real-data budget is
+spent two ways: **uniform** (spread evenly over all 10 regions) vs **matched** (concentrated on the
+"exercised" region we want to protect). One region is designated exercised (region 0 here) and has a
+rare tail we track.
+
+### Symbols
+- **region** — a block of related items; a stand-in for a task family / subject area.
+- **matched vs uniform** — real data aimed at the exercised region vs spread evenly, at equal total budget.
+- **tail items alive** — how many rare items in a region still have any probability.
+
+### The two panels
+1. **Target region over time.** Rare-item survival in the exercised region, generation by generation:
+   blue = matched, red = uniform (bands = 95% CI). Matched **holds** the region's tail alive; uniform
+   spreads too thin and lets it **collapse**.
+2. **Every region at steady state.** Bar chart of stationary tail survival per region, matched (blue)
+   vs uniform (red); the dotted line marks the exercised region. Matched wins big *there* — at the
+   cost of the regions it deliberately ignores. Uniform is mediocre everywhere.
+
+*(Note: per-region diversity `H` is confounded by how much probability mass sits in a region, so this
+figure uses the honest, mass-independent metric — tail-item survival.)*
+
+### Takeaway
+Reality checks only protect what they actually cover. To keep a capability alive you must ground
+**on that capability**, not on data in general — grounding is local, not a global tonic. Key numbers:
+exercised-region tail survival ≈ **0.49 (matched)** vs **0.07 (uniform)** at equal budget.
+**Falsifier (not triggered):** if uniform had protected the region as well as matched, the
+targeting claim would die.

results/figS5_aimed_grounding/manifest.json

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+{
+  "experiment": "E3_region_matched_grounding",
+  "master_seed": 20260704,
+  "git_commit": "a6eb9b75124779375fa1a0b3a64115ecd705b218",
+  "python": "3.14.5",
+  "libraries": {
+    "numpy": "2.5.0",
+    "scipy": "1.18.0",
+    "pandas": "3.0.3",
+    "pyarrow": "24.0.0"
+  },
+  "rows": 80200,
+  "results_sha256": "7ae056faf8db591a913087004068d0e732f10b0244cdc6a78bb72a691f4b8604"
+}

results/figS5_aimed_grounding/resolved_config.yaml

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+experiment: E3_region_matched_grounding
+seed: 20260704
+n_replicates: 100
+source_config:
+  experiment: E3_region_matched_grounding
+  seed: 20260704
+  n_replicates: 100
+  generations: 400
+  truth:
+    K: 1000
+    R: 10
+    tail: zipf
+    zipf_s: 1.1
+    tail_frac: 0.5
+    tail_threshold: 0.001
+    init: truth
+  dynamics:
+    n: 200
+    teachers:
+      K_T: 1
+      rho: 0.0
+      q: 1.0
+    grounding:
+      m: 100
+      policy: uniform
+      exercised:
+      - 0
+    selection:
+      mode: none
+      novelty_alpha: 0.0
+    remint:
+      enabled: false
+      period: null
+      H_gate: null
+  metrics:
+    kl_floor: 1.0e-09
+    support_eps: 1.0e-09
+  sweep:
+  - param: dynamics.grounding.policy
+    values:
+    - uniform
+    - matched
+  output:
+    dir: results/figS5_aimed_grounding
+grid:
+- label:
+    policy: uniform
+  lineage_cfg:
+    truth:
+      K: 1000
+      R: 10
+      tail: zipf
+      zipf_s: 1.1
+      tail_frac: 0.5
+      tail_threshold: 0.001
+      init: truth
+    dynamics:
+      n: 200
+      teachers:
+        K_T: 1
+        rho: 0.0
+        q: 1.0
+      grounding:
+        m: 100
+        policy: uniform
+        exercised:
+        - 0
+      selection:
+        mode: none
+        novelty_alpha: 0.0
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 400
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09
+- label:
+    policy: matched
+  lineage_cfg:
+    truth:
+      K: 1000
+      R: 10
+      tail: zipf
+      zipf_s: 1.1
+      tail_frac: 0.5
+      tail_threshold: 0.001
+      init: truth
+    dynamics:
+      n: 200
+      teachers:
+        K_T: 1
+        rho: 0.0
+        q: 1.0
+      grounding:
+        m: 100
+        policy: matched
+        exercised:
+        - 0
+      selection:
+        mode: none
+        novelty_alpha: 0.0
+      remint:
+        enabled: false
+        period: null
+        H_gate: null
+    generations: 400
+    metrics:
+      kl_floor: 1.0e-09
+      support_eps: 1.0e-09