Refactor: Modularize code structure for better maintainability

- Split HMM module into separate files (emission.rs, config.rs, model.rs, viterbi.rs, python_bindings.rs)
- Split MCMC module into separate files (proposal.rs, config.rs, likelihood.rs, sampler.rs, python_bindings.rs)
- Create organized src/hmm/ and src/mcmc/ directory structure
- Rename legacy files to hmm_legacy.rs and mcmc_legacy.rs for backward compatibility
- Update lib.rs to use new modular structure
- Reduce file sizes: largest file now 171 lines (previously 583 lines)
- Improve code reusability and maintainability
- All Python bindings remain backward compatible

src/mcmc/likelihood.rs

@@ -0,0 +1,53 @@
+//! Log-likelihood interface for MCMC
+//!
+//! Defines the LogLikelihood trait for target distributions.
+
+use pyo3::prelude::*;
+
+/// Generic log-likelihood function trait
+pub trait LogLikelihood: Send + Sync {
+    fn evaluate(&self, state: &[f64]) -> f64;
+}
+
+/// Wrapper for Python callable log-likelihood
+pub struct PyLogLikelihood {
+    func: Py<PyAny>,
+}
+
+impl PyLogLikelihood {
+    pub fn new(func: Py<PyAny>) -> Self {
+        Self { func }
+    }
+}
+
+impl LogLikelihood for PyLogLikelihood {
+    fn evaluate(&self, state: &[f64]) -> f64 {
+        Python::with_gil(|py| {
+            let args = (state.to_vec(),);
+            self.func
+                .call1(py, args)
+                .and_then(|res| res.extract::<f64>(py))
+                .unwrap_or(f64::NEG_INFINITY)
+        })
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    struct TestLogLikelihood;
+    
+    impl LogLikelihood for TestLogLikelihood {
+        fn evaluate(&self, state: &[f64]) -> f64 {
+            // Standard normal log-likelihood
+            -0.5 * state.iter().map(|x| x.powi(2)).sum::<f64>()
+        }
+    }
+
+    #[test]
+    fn test_log_likelihood() {
+        let ll = TestLogLikelihood;
+        assert!(ll.evaluate(&[0.0]) > ll.evaluate(&[1.0]));
+    }
+}