Fix docs: flat YAML format, correct class/param names, CLI accuracy

[cweniger]

Summary

Two-pass audit of all documentation against the actual source code, fixing incorrect or misleading content that would cause failures if followed verbatim.

Critical fixes

• Flat YAML format (docs/api/flow.md, docs/api/gaussian.md, docs/configuration.md, docs/getting-started.md): The docs described fictional nested YAML groups (loop:, network:, optimizer:, inference:) under estimator:. These keys are not valid Flow.__init__ arguments and would raise TypeError at runtime. All examples now use the correct flat format matching the actual working examples in examples/.

• Class name Gaussian → GaussianFullCov (multiple files): The class Gaussian was never defined or exported — only GaussianFullCov exists in gaussian_fullcov.py. from falcon.estimators import Gaussian would raise AttributeError.

• DiagonalWhitener YAML example (docs/api/embeddings.md): Missing required dim argument — would raise TypeError on instantiation.

Parameter name fixes

• scheduler_patience → lr_patience (actual Flow/GaussianFullCov param)
• use_best_models_during_inference → use_best_models
• Logged metric names: loss/train → train:loss, loss/val → val:loss, best_val_loss → checkpoint:conditional / checkpoint:marginal
• buffer.max_epochs (nonexistent) → buffer.max_samples in CLI override example

Installation / CLI fixes

• pip install -e ".[monitor]" → ".[all]" in README ([monitor] extra never existed)
• pip install -e . → ".[all]" in docs/index.md (bare install lacks sbi, which Flow requires)
• paths.import → paths.imports (correct key name, list type)
• Python 3.9+ → Python 3.10+ (matches pyproject.toml)
• Removed falcon monitor from CLI table (doesn't exist; TUI launches automatically in falcon launch)
• Added ppd to falcon sample synopsis

Missing / incomplete API docs

• setup() added to BaseEstimator members list (it is @abstractmethod)
• add_node() added to Graph members list (main Python API for programmatic graph construction)
• Removed non-existent FlowConfig, NetworkConfig, OptimizerConfig, InferenceConfig class references from flow.md
• Added missing Flow parameters: prior_epochs, betas, device
• Added undocumented buffer fields: simulate_chunk_size, initial_samples_path
• lognormal distribution: noted it only works with mode="standard_normal" (raises ValueError with mode="hypercube")
• Updated package tree in api/index.md: gaussian_fullcov, stepwise_base, networks, embedded_posterior
• Fixed GaussianFullCov class reference path (gaussian_fullcov module, not gaussian)

Test plan

• Verify YAML examples in docs/getting-started.md and docs/configuration.md run without error against examples/01_minimal
• Verify from falcon.estimators import GaussianFullCov succeeds
• Verify falcon sample ppd is accepted by the CLI
• Build docs site and confirm no broken mkdocstrings references

🤖 Generated with Claude Code

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 10.42%. Comparing base (6560353) to head (e252be9).
⚠️ Report is 2 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #106   +/-   ##
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  Coverage   10.42%   10.42%           
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  Files          30       30           
  Lines        3896     3896           
=======================================
  Hits          406      406           
  Misses       3490     3490           

Flag	Coverage Δ
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