diff --git a/AGENTS.md b/AGENTS.md
index 0912a246..23f8cd7d 100644
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -169,17 +169,24 @@ Tree-sitter: `((a) (b))` — Plotnik: `{(a) (b)}`. The #1 syntax error.
 ```
 crates/
   plotnik-cli/         # CLI tool
-    src/commands/      # Subcommands (debug, exec, langs, types)
-  plotnik-core/        # Common code
+    src/commands/      # Subcommands (check, dump, infer, tree, langs)
+  plotnik-core/        # Common code (Interner, Symbol)
   plotnik-lib/         # Plotnik as library
     src/
-      diagnostics/     # Diagnostics (user-friendly errors)
-      parser/          # Syntactic parsing of the query
-      query/           # Analysis and representation of the parsed query
-  plotnik-langs/       # Tree-sitter language bindings (wrapped)
-  plotnik-macros/      # Proc macros of the project
+      analyze/         # Semantic analysis (symbol_table, dependencies, type_check, validation)
+      bytecode/        # Binary format definitions
+      typegen/         # Type declaration extraction (bytecode → .d.ts)
+      compile/         # Thompson NFA construction (AST → IR)
+      diagnostics/     # User-friendly error reporting
+      emit/            # Bytecode emission (IR → binary)
+      parser/          # Syntactic parsing (lexer, grammar, AST)
+      query/           # Query facade (Query, QueryBuilder, SourceMap)
+      type_system/     # Shared type primitives
+  plotnik-langs/       # Tree-sitter language bindings
+  plotnik-macros/      # Proc macros
 docs/
-  adr/                 # Architecture Decision Records (ADRs)
+  adr/                 # Architecture Decision Records
+  binary-format/       # Bytecode format specification
   lang-reference.md    # Language specification
 ```
 
diff --git a/crates/plotnik-cli/src/commands/infer.rs b/crates/plotnik-cli/src/commands/infer.rs
index 8cfe02cc..839201b3 100644
--- a/crates/plotnik-cli/src/commands/infer.rs
+++ b/crates/plotnik-cli/src/commands/infer.rs
@@ -4,7 +4,7 @@ use std::path::PathBuf;
 
 use plotnik_lib::QueryBuilder;
 use plotnik_lib::bytecode::Module;
-use plotnik_lib::codegen::typescript;
+use plotnik_lib::typegen::typescript;
 
 use super::lang_resolver::{resolve_lang, resolve_lang_required, suggest_language};
 use super::query_loader::load_query_source;
diff --git a/crates/plotnik-lib/src/query/dependencies.rs b/crates/plotnik-lib/src/analyze/dependencies.rs
similarity index 99%
rename from crates/plotnik-lib/src/query/dependencies.rs
rename to crates/plotnik-lib/src/analyze/dependencies.rs
index 2ee73529..2437bb67 100644
--- a/crates/plotnik-lib/src/query/dependencies.rs
+++ b/crates/plotnik-lib/src/analyze/dependencies.rs
@@ -12,16 +12,15 @@ use std::collections::{HashMap, HashSet};
 
 use indexmap::{IndexMap, IndexSet};
 use plotnik_core::{Interner, Symbol};
-
-use super::source_map::SourceId;
 use rowan::TextRange;
 
+use super::symbol_table::SymbolTable;
+use super::type_check::DefId;
+use super::visitor::{Visitor, walk_expr};
 use crate::Diagnostics;
 use crate::diagnostics::DiagnosticKind;
 use crate::parser::{AnonymousNode, Def, Expr, NamedNode, Ref, Root, SeqExpr};
-use crate::query::symbol_table::SymbolTable;
-use crate::query::type_check::DefId;
-use crate::query::visitor::{Visitor, walk_expr};
+use crate::query::source_map::SourceId;
 
 /// Result of dependency analysis.
 #[derive(Clone, Debug, Default)]
diff --git a/crates/plotnik-lib/src/query/dependencies_tests.rs b/crates/plotnik-lib/src/analyze/dependencies_tests.rs
similarity index 100%
rename from crates/plotnik-lib/src/query/dependencies_tests.rs
rename to crates/plotnik-lib/src/analyze/dependencies_tests.rs
diff --git a/crates/plotnik-lib/src/query/invariants.rs b/crates/plotnik-lib/src/analyze/invariants.rs
similarity index 100%
rename from crates/plotnik-lib/src/query/invariants.rs
rename to crates/plotnik-lib/src/analyze/invariants.rs
diff --git a/crates/plotnik-lib/src/query/link.rs b/crates/plotnik-lib/src/analyze/link.rs
similarity index 99%
rename from crates/plotnik-lib/src/query/link.rs
rename to crates/plotnik-lib/src/analyze/link.rs
index 84107723..820c2eab 100644
--- a/crates/plotnik-lib/src/query/link.rs
+++ b/crates/plotnik-lib/src/analyze/link.rs
@@ -20,16 +20,15 @@ pub struct LinkOutput {
     pub node_field_ids: IndexMap<Symbol, NodeFieldId>,
 }
 
+use super::symbol_table::SymbolTable;
+use super::utils::find_similar;
+use super::visitor::{Visitor, walk};
 use crate::diagnostics::{DiagnosticKind, Diagnostics};
 use crate::parser::ast::{self, Expr, NamedNode};
 use crate::parser::cst::{SyntaxKind, SyntaxToken};
 use crate::parser::token_src;
-
-use super::query::AstMap;
-use super::source_map::{SourceId, SourceMap};
-use super::symbol_table::SymbolTable;
-use super::utils::find_similar;
-use super::visitor::{Visitor, walk};
+use crate::query::query::AstMap;
+use crate::query::source_map::{SourceId, SourceMap};
 
 /// Link query against a language grammar.
 ///
diff --git a/crates/plotnik-lib/src/query/link_tests.rs b/crates/plotnik-lib/src/analyze/link_tests.rs
similarity index 100%
rename from crates/plotnik-lib/src/query/link_tests.rs
rename to crates/plotnik-lib/src/analyze/link_tests.rs
diff --git a/crates/plotnik-lib/src/analyze/mod.rs b/crates/plotnik-lib/src/analyze/mod.rs
new file mode 100644
index 00000000..f487cede
--- /dev/null
+++ b/crates/plotnik-lib/src/analyze/mod.rs
@@ -0,0 +1,32 @@
+//! Semantic analysis passes.
+//!
+//! Provides analysis passes that transform parsed AST into analyzed form:
+//! - Name resolution (symbol_table)
+//! - Dependency analysis and recursion detection (dependencies)
+//! - Type inference (type_check)
+//! - Grammar linking (link)
+//! - Semantic validation (validation)
+
+pub mod dependencies;
+mod invariants;
+pub mod link;
+pub mod refs;
+pub mod symbol_table;
+pub mod type_check;
+mod utils;
+pub mod validation;
+pub mod visitor;
+
+#[cfg(test)]
+mod dependencies_tests;
+#[cfg(all(test, feature = "plotnik-langs"))]
+mod link_tests;
+#[cfg(test)]
+mod symbol_table_tests;
+
+pub use dependencies::DependencyAnalysis;
+pub use link::LinkOutput;
+pub use symbol_table::{SymbolTable, UNNAMED_DEF};
+pub use type_check::{TypeContext, infer_types, primary_def_name};
+pub use validation::{validate_alt_kinds, validate_anchors};
+pub use visitor::{Visitor, walk_expr};
diff --git a/crates/plotnik-lib/src/query/refs.rs b/crates/plotnik-lib/src/analyze/refs.rs
similarity index 100%
rename from crates/plotnik-lib/src/query/refs.rs
rename to crates/plotnik-lib/src/analyze/refs.rs
diff --git a/crates/plotnik-lib/src/query/symbol_table.rs b/crates/plotnik-lib/src/analyze/symbol_table.rs
similarity index 99%
rename from crates/plotnik-lib/src/query/symbol_table.rs
rename to crates/plotnik-lib/src/analyze/symbol_table.rs
index 7bd530c5..e83fdc7f 100644
--- a/crates/plotnik-lib/src/query/symbol_table.rs
+++ b/crates/plotnik-lib/src/analyze/symbol_table.rs
@@ -10,8 +10,8 @@ use crate::Diagnostics;
 use crate::diagnostics::DiagnosticKind;
 use crate::parser::{Root, ast, token_src};
 
-use super::source_map::{SourceId, SourceMap};
 use super::visitor::Visitor;
+use crate::query::source_map::{SourceId, SourceMap};
 
 /// Sentinel name for unnamed definitions (bare expressions at root level).
 /// Code generators can emit whatever name they want for this.
diff --git a/crates/plotnik-lib/src/query/symbol_table_tests.rs b/crates/plotnik-lib/src/analyze/symbol_table_tests.rs
similarity index 100%
rename from crates/plotnik-lib/src/query/symbol_table_tests.rs
rename to crates/plotnik-lib/src/analyze/symbol_table_tests.rs
diff --git a/crates/plotnik-lib/src/query/type_check/context.rs b/crates/plotnik-lib/src/analyze/type_check/context.rs
similarity index 99%
rename from crates/plotnik-lib/src/query/type_check/context.rs
rename to crates/plotnik-lib/src/analyze/type_check/context.rs
index 92533ce0..fa5685ea 100644
--- a/crates/plotnik-lib/src/query/type_check/context.rs
+++ b/crates/plotnik-lib/src/analyze/type_check/context.rs
@@ -233,7 +233,6 @@ mod tests {
     use std::collections::BTreeMap;
 
     use super::*;
-    use crate::query::type_check::types::FieldInfo;
 
     #[test]
     fn builtin_types_have_correct_ids() {
diff --git a/crates/plotnik-lib/src/query/type_check/infer.rs b/crates/plotnik-lib/src/analyze/type_check/infer.rs
similarity index 99%
rename from crates/plotnik-lib/src/query/type_check/infer.rs
rename to crates/plotnik-lib/src/analyze/type_check/infer.rs
index ab8954a0..d6baac3a 100644
--- a/crates/plotnik-lib/src/query/type_check/infer.rs
+++ b/crates/plotnik-lib/src/analyze/type_check/infer.rs
@@ -16,6 +16,8 @@ use super::types::{
 };
 use super::unify::{UnifyError, unify_flows};
 
+use crate::analyze::symbol_table::SymbolTable;
+use crate::analyze::visitor::{Visitor, walk_alt_expr, walk_def, walk_named_node, walk_seq_expr};
 use crate::diagnostics::{DiagnosticKind, Diagnostics};
 use crate::parser::ast::{
     AltExpr, AltKind, AnonymousNode, CapturedExpr, Def, Expr, FieldExpr, NamedNode, QuantifiedExpr,
@@ -23,8 +25,6 @@ use crate::parser::ast::{
 };
 use crate::parser::cst::SyntaxKind;
 use crate::query::source_map::SourceId;
-use crate::query::symbol_table::SymbolTable;
-use crate::query::visitor::{Visitor, walk_alt_expr, walk_def, walk_named_node, walk_seq_expr};
 
 /// Inference context for a single pass over the AST.
 pub struct InferenceVisitor<'a, 'd> {
diff --git a/crates/plotnik-lib/src/query/type_check/mod.rs b/crates/plotnik-lib/src/analyze/type_check/mod.rs
similarity index 96%
rename from crates/plotnik-lib/src/query/type_check/mod.rs
rename to crates/plotnik-lib/src/analyze/type_check/mod.rs
index 66932018..5134a751 100644
--- a/crates/plotnik-lib/src/query/type_check/mod.rs
+++ b/crates/plotnik-lib/src/analyze/type_check/mod.rs
@@ -6,7 +6,7 @@
 mod context;
 mod infer;
 mod symbol;
-mod types;
+pub(crate) mod types;
 mod unify;
 
 #[cfg(test)]
@@ -24,11 +24,11 @@ use std::collections::BTreeMap;
 
 use indexmap::IndexMap;
 
+use crate::analyze::dependencies::DependencyAnalysis;
+use crate::analyze::symbol_table::{SymbolTable, UNNAMED_DEF};
 use crate::diagnostics::Diagnostics;
 use crate::parser::ast::Root;
-use crate::query::dependencies::DependencyAnalysis;
 use crate::query::source_map::SourceId;
-use crate::query::symbol_table::{SymbolTable, UNNAMED_DEF};
 
 use infer::infer_root;
 
diff --git a/crates/plotnik-lib/src/query/type_check/symbol.rs b/crates/plotnik-lib/src/analyze/type_check/symbol.rs
similarity index 100%
rename from crates/plotnik-lib/src/query/type_check/symbol.rs
rename to crates/plotnik-lib/src/analyze/type_check/symbol.rs
diff --git a/crates/plotnik-lib/src/query/type_check/tests.rs b/crates/plotnik-lib/src/analyze/type_check/tests.rs
similarity index 100%
rename from crates/plotnik-lib/src/query/type_check/tests.rs
rename to crates/plotnik-lib/src/analyze/type_check/tests.rs
diff --git a/crates/plotnik-lib/src/query/type_check/types.rs b/crates/plotnik-lib/src/analyze/type_check/types.rs
similarity index 100%
rename from crates/plotnik-lib/src/query/type_check/types.rs
rename to crates/plotnik-lib/src/analyze/type_check/types.rs
diff --git a/crates/plotnik-lib/src/query/type_check/unify.rs b/crates/plotnik-lib/src/analyze/type_check/unify.rs
similarity index 99%
rename from crates/plotnik-lib/src/query/type_check/unify.rs
rename to crates/plotnik-lib/src/analyze/type_check/unify.rs
index f44014b5..444e88ec 100644
--- a/crates/plotnik-lib/src/query/type_check/unify.rs
+++ b/crates/plotnik-lib/src/analyze/type_check/unify.rs
@@ -143,7 +143,7 @@ fn unify_type_ids(a: TypeId, b: TypeId, field: Symbol) -> Result<TypeId, UnifyEr
 #[cfg(test)]
 mod tests {
     use super::*;
-    use crate::query::type_check::TYPE_NODE;
+    use crate::analyze::type_check::TYPE_NODE;
     use plotnik_core::Interner;
 
     #[test]
diff --git a/crates/plotnik-lib/src/query/utils.rs b/crates/plotnik-lib/src/analyze/utils.rs
similarity index 100%
rename from crates/plotnik-lib/src/query/utils.rs
rename to crates/plotnik-lib/src/analyze/utils.rs
diff --git a/crates/plotnik-lib/src/query/alt_kinds.rs b/crates/plotnik-lib/src/analyze/validation/alt_kinds.rs
similarity index 94%
rename from crates/plotnik-lib/src/query/alt_kinds.rs
rename to crates/plotnik-lib/src/analyze/validation/alt_kinds.rs
index e9645af8..d5c7cc8c 100644
--- a/crates/plotnik-lib/src/query/alt_kinds.rs
+++ b/crates/plotnik-lib/src/analyze/validation/alt_kinds.rs
@@ -3,9 +3,9 @@
 //! Checks constraints that are easier to express after parsing:
 //! - Mixed tagged/untagged alternations
 
-use super::invariants::ensure_both_branch_kinds;
-use super::visitor::{Visitor, walk, walk_alt_expr};
 use crate::SourceId;
+use crate::analyze::invariants::ensure_both_branch_kinds;
+use crate::analyze::visitor::{Visitor, walk, walk_alt_expr};
 use crate::diagnostics::{DiagnosticKind, Diagnostics};
 use crate::parser::{AltExpr, AltKind, Branch, Root};
 
diff --git a/crates/plotnik-lib/src/query/alt_kinds_tests.rs b/crates/plotnik-lib/src/analyze/validation/alt_kinds_tests.rs
similarity index 100%
rename from crates/plotnik-lib/src/query/alt_kinds_tests.rs
rename to crates/plotnik-lib/src/analyze/validation/alt_kinds_tests.rs
diff --git a/crates/plotnik-lib/src/query/anchors.rs b/crates/plotnik-lib/src/analyze/validation/anchors.rs
similarity index 96%
rename from crates/plotnik-lib/src/query/anchors.rs
rename to crates/plotnik-lib/src/analyze/validation/anchors.rs
index 4bcc1ec3..065ea063 100644
--- a/crates/plotnik-lib/src/query/anchors.rs
+++ b/crates/plotnik-lib/src/analyze/validation/anchors.rs
@@ -6,8 +6,8 @@
 //!
 //! This validation ensures anchors are placed where they can be meaningfully compiled.
 
-use super::visitor::{Visitor, walk_named_node, walk_seq_expr};
 use crate::SourceId;
+use crate::analyze::visitor::{Visitor, walk_named_node, walk_seq_expr};
 use crate::diagnostics::{DiagnosticKind, Diagnostics};
 use crate::parser::ast::{NamedNode, Root, SeqExpr, SeqItem};
 
diff --git a/crates/plotnik-lib/src/query/anchors_tests.rs b/crates/plotnik-lib/src/analyze/validation/anchors_tests.rs
similarity index 100%
rename from crates/plotnik-lib/src/query/anchors_tests.rs
rename to crates/plotnik-lib/src/analyze/validation/anchors_tests.rs
diff --git a/crates/plotnik-lib/src/analyze/validation/mod.rs b/crates/plotnik-lib/src/analyze/validation/mod.rs
new file mode 100644
index 00000000..1c1354f2
--- /dev/null
+++ b/crates/plotnik-lib/src/analyze/validation/mod.rs
@@ -0,0 +1,16 @@
+//! Semantic validation passes.
+//!
+//! Validates semantic constraints that aren't captured by parsing or type checking:
+//! - Alternation kind consistency (alt_kinds)
+//! - Anchor placement rules (anchors)
+
+pub mod alt_kinds;
+pub mod anchors;
+
+#[cfg(test)]
+mod alt_kinds_tests;
+#[cfg(test)]
+mod anchors_tests;
+
+pub use alt_kinds::validate_alt_kinds;
+pub use anchors::validate_anchors;
diff --git a/crates/plotnik-lib/src/query/visitor.rs b/crates/plotnik-lib/src/analyze/visitor.rs
similarity index 100%
rename from crates/plotnik-lib/src/query/visitor.rs
rename to crates/plotnik-lib/src/analyze/visitor.rs
diff --git a/crates/plotnik-lib/src/bytecode/emit/mod.rs b/crates/plotnik-lib/src/bytecode/emit/mod.rs
deleted file mode 100644
index ec604807..00000000
--- a/crates/plotnik-lib/src/bytecode/emit/mod.rs
+++ /dev/null
@@ -1,10 +0,0 @@
-//! Code generation from bytecode Module.
-//!
-//! This module re-exports from [`crate::codegen`] for backwards compatibility.
-//! New code should use [`crate::codegen::typescript`] directly.
-
-// Re-export from codegen module for backwards compatibility
-pub use crate::codegen::typescript::{
-    Config as TsEmitConfig, Emitter as TsEmitter, emit as emit_typescript,
-    emit_with_config as emit_typescript_with_config,
-};
diff --git a/crates/plotnik-lib/src/bytecode/ir.rs b/crates/plotnik-lib/src/bytecode/ir.rs
index 643c9d06..c40ccac2 100644
--- a/crates/plotnik-lib/src/bytecode/ir.rs
+++ b/crates/plotnik-lib/src/bytecode/ir.rs
@@ -11,7 +11,7 @@ use super::effects::{EffectOp, EffectOpcode};
 use super::ids::StepId;
 use super::instructions::{Call, Match, Return, select_match_opcode};
 use super::nav::Nav;
-use crate::query::type_check::TypeId;
+use crate::analyze::type_check::TypeId;
 
 /// Symbolic reference, resolved to StepId at layout time.
 #[derive(Clone, Copy, PartialEq, Eq, PartialOrd, Ord, Hash, Debug)]
diff --git a/crates/plotnik-lib/src/bytecode/mod.rs b/crates/plotnik-lib/src/bytecode/mod.rs
index 9fdf7557..daa8979e 100644
--- a/crates/plotnik-lib/src/bytecode/mod.rs
+++ b/crates/plotnik-lib/src/bytecode/mod.rs
@@ -5,13 +5,11 @@
 mod constants;
 mod dump;
 mod effects;
-pub mod emit;
 mod entrypoint;
 mod header;
 mod ids;
 mod instructions;
 pub mod ir;
-pub mod layout;
 mod module;
 mod nav;
 mod sections;
@@ -52,6 +50,4 @@ mod dump_tests;
 #[cfg(test)]
 mod instructions_tests;
 #[cfg(test)]
-mod layout_tests;
-#[cfg(test)]
 mod module_tests;
diff --git a/crates/plotnik-lib/src/codegen/mod.rs b/crates/plotnik-lib/src/codegen/mod.rs
deleted file mode 100644
index cebcc363..00000000
--- a/crates/plotnik-lib/src/codegen/mod.rs
+++ /dev/null
@@ -1,21 +0,0 @@
-//! Code generation from bytecode Module.
-//!
-//! This module provides emitters for generating code from compiled bytecode.
-//! Each target language has its own submodule with a `Config` struct and `emit()` function.
-//!
-//! # Example
-//!
-//! ```ignore
-//! use plotnik_lib::codegen::typescript;
-//! use plotnik_lib::bytecode::Module;
-//!
-//! let module = Module::from_bytes(bytecode)?;
-//! let config = typescript::Config {
-//!     export: true,
-//!     emit_node_type: true,
-//!     verbose_nodes: false,
-//! };
-//! let output = typescript::emit_with_config(&module, config);
-//! ```
-
-pub mod typescript;
diff --git a/crates/plotnik-lib/src/query/compile/capture.rs b/crates/plotnik-lib/src/compile/capture.rs
similarity index 99%
rename from crates/plotnik-lib/src/query/compile/capture.rs
rename to crates/plotnik-lib/src/compile/capture.rs
index 94432efa..90e9ba72 100644
--- a/crates/plotnik-lib/src/query/compile/capture.rs
+++ b/crates/plotnik-lib/src/compile/capture.rs
@@ -8,7 +8,7 @@ use std::collections::HashSet;
 use crate::bytecode::ir::EffectIR;
 use crate::bytecode::EffectOpcode;
 use crate::parser::ast::{self, Expr};
-use crate::query::type_check::{TypeContext, TypeId, TypeShape};
+use crate::analyze::type_check::{TypeContext, TypeId, TypeShape};
 
 use super::navigation::{inner_creates_scope, is_star_or_plus_quantifier};
 use super::Compiler;
diff --git a/crates/plotnik-lib/src/query/compile/expressions.rs b/crates/plotnik-lib/src/compile/expressions.rs
similarity index 99%
rename from crates/plotnik-lib/src/query/compile/expressions.rs
rename to crates/plotnik-lib/src/compile/expressions.rs
index 2d23b46f..8d92fd26 100644
--- a/crates/plotnik-lib/src/query/compile/expressions.rs
+++ b/crates/plotnik-lib/src/compile/expressions.rs
@@ -12,7 +12,7 @@ use std::num::NonZeroU16;
 use crate::bytecode::ir::{CallIR, Instruction, Label, MatchIR};
 use crate::bytecode::Nav;
 use crate::parser::ast::{self, Expr};
-use crate::query::type_check::Arity;
+use crate::analyze::type_check::Arity;
 
 use super::capture::CaptureEffects;
 use super::navigation::{check_trailing_anchor, inner_creates_scope, is_skippable_quantifier, is_star_or_plus_quantifier};
diff --git a/crates/plotnik-lib/src/query/compile/mod.rs b/crates/plotnik-lib/src/compile/mod.rs
similarity index 98%
rename from crates/plotnik-lib/src/query/compile/mod.rs
rename to crates/plotnik-lib/src/compile/mod.rs
index 86037865..f5c4ab0d 100644
--- a/crates/plotnik-lib/src/query/compile/mod.rs
+++ b/crates/plotnik-lib/src/compile/mod.rs
@@ -28,9 +28,9 @@ use crate::bytecode::ir::{Instruction, Label, ReturnIR};
 use crate::bytecode::Nav;
 use crate::parser::ast::Expr;
 
-use super::codegen::StringTableBuilder;
-use super::symbol_table::SymbolTable;
-use super::type_check::{DefId, TypeContext};
+use crate::emit::StringTableBuilder;
+use crate::analyze::symbol_table::SymbolTable;
+use crate::analyze::type_check::{DefId, TypeContext};
 
 pub use capture::CaptureEffects;
 use scope::StructScope;
diff --git a/crates/plotnik-lib/src/query/compile/navigation.rs b/crates/plotnik-lib/src/compile/navigation.rs
similarity index 100%
rename from crates/plotnik-lib/src/query/compile/navigation.rs
rename to crates/plotnik-lib/src/compile/navigation.rs
diff --git a/crates/plotnik-lib/src/query/compile/quantifier.rs b/crates/plotnik-lib/src/compile/quantifier.rs
similarity index 99%
rename from crates/plotnik-lib/src/query/compile/quantifier.rs
rename to crates/plotnik-lib/src/compile/quantifier.rs
index 4909faa5..3e014c9b 100644
--- a/crates/plotnik-lib/src/query/compile/quantifier.rs
+++ b/crates/plotnik-lib/src/compile/quantifier.rs
@@ -10,7 +10,7 @@ use crate::bytecode::ir::{EffectIR, Label};
 use crate::bytecode::{EffectOpcode, Nav};
 use crate::parser::ast::{self, Expr};
 use crate::parser::cst::SyntaxKind;
-use crate::query::type_check::TypeId;
+use crate::analyze::type_check::TypeId;
 
 use super::capture::{check_needs_struct_wrapper, get_row_type_id, CaptureEffects};
 use super::navigation::{is_star_or_plus_quantifier, repeat_nav_for};
diff --git a/crates/plotnik-lib/src/query/compile/scope.rs b/crates/plotnik-lib/src/compile/scope.rs
similarity index 99%
rename from crates/plotnik-lib/src/query/compile/scope.rs
rename to crates/plotnik-lib/src/compile/scope.rs
index be5280bd..ec6bfada 100644
--- a/crates/plotnik-lib/src/query/compile/scope.rs
+++ b/crates/plotnik-lib/src/compile/scope.rs
@@ -5,7 +5,7 @@
 use crate::bytecode::ir::{EffectIR, Instruction, Label, MatchIR, MemberRef};
 use crate::bytecode::{EffectOpcode, Nav};
 use crate::parser::ast::Expr;
-use crate::query::type_check::TypeId;
+use crate::analyze::type_check::TypeId;
 
 use super::capture::CaptureEffects;
 use super::Compiler;
diff --git a/crates/plotnik-lib/src/query/compile/sequences.rs b/crates/plotnik-lib/src/compile/sequences.rs
similarity index 99%
rename from crates/plotnik-lib/src/query/compile/sequences.rs
rename to crates/plotnik-lib/src/compile/sequences.rs
index bafbca17..e891e5bd 100644
--- a/crates/plotnik-lib/src/query/compile/sequences.rs
+++ b/crates/plotnik-lib/src/compile/sequences.rs
@@ -7,7 +7,7 @@
 use crate::bytecode::ir::{EffectIR, Instruction, Label, MatchIR, MemberRef};
 use crate::bytecode::{EffectOpcode, Nav};
 use crate::parser::ast::{self, Expr, SeqItem};
-use crate::query::type_check::TypeShape;
+use crate::analyze::type_check::TypeShape;
 
 use super::capture::CaptureEffects;
 use super::navigation::{compute_nav_modes, is_down_nav, is_skippable_quantifier, repeat_nav_for};
diff --git a/crates/plotnik-lib/src/query/codegen_tests.rs b/crates/plotnik-lib/src/emit/codegen_tests.rs
similarity index 98%
rename from crates/plotnik-lib/src/query/codegen_tests.rs
rename to crates/plotnik-lib/src/emit/codegen_tests.rs
index 54986180..f1845428 100644
--- a/crates/plotnik-lib/src/query/codegen_tests.rs
+++ b/crates/plotnik-lib/src/emit/codegen_tests.rs
@@ -4,7 +4,7 @@ use indoc::indoc;
 
 use crate::Query;
 use crate::bytecode::{Header, MAGIC, Module, QTypeId, VERSION};
-use crate::query::codegen::{StringTableBuilder, TypeTableBuilder};
+use super::{StringTableBuilder, TypeTableBuilder};
 
 #[test]
 fn emit_minimal_query() {
@@ -182,12 +182,12 @@ fn string_table_builder_intern_str() {
 
 #[test]
 fn type_table_builder_builtins() {
-    use crate::query::type_check::{TYPE_NODE, TYPE_STRING, TYPE_VOID};
+    use crate::analyze::type_check::{TYPE_NODE, TYPE_STRING, TYPE_VOID};
 
     let mut builder = TypeTableBuilder::new();
 
     // Build with empty context
-    let type_ctx = crate::query::type_check::TypeContext::new();
+    let type_ctx = crate::analyze::type_check::TypeContext::new();
     let interner = plotnik_core::Interner::new();
     let mut strings = StringTableBuilder::new();
 
diff --git a/crates/plotnik-lib/src/bytecode/layout.rs b/crates/plotnik-lib/src/emit/layout.rs
similarity index 98%
rename from crates/plotnik-lib/src/bytecode/layout.rs
rename to crates/plotnik-lib/src/emit/layout.rs
index acadf972..68835622 100644
--- a/crates/plotnik-lib/src/bytecode/layout.rs
+++ b/crates/plotnik-lib/src/emit/layout.rs
@@ -5,8 +5,8 @@
 
 use std::collections::{BTreeMap, HashSet};
 
-use super::ids::StepId;
-use super::ir::{Instruction, Label, LayoutResult};
+use crate::bytecode::StepId;
+use crate::bytecode::ir::{Instruction, Label, LayoutResult};
 
 const CACHE_LINE: usize = 64;
 const STEP_SIZE: usize = 8;
diff --git a/crates/plotnik-lib/src/bytecode/layout_tests.rs b/crates/plotnik-lib/src/emit/layout_tests.rs
similarity index 97%
rename from crates/plotnik-lib/src/bytecode/layout_tests.rs
rename to crates/plotnik-lib/src/emit/layout_tests.rs
index 690a18dc..3d518db5 100644
--- a/crates/plotnik-lib/src/bytecode/layout_tests.rs
+++ b/crates/plotnik-lib/src/emit/layout_tests.rs
@@ -1,10 +1,10 @@
 use std::num::NonZeroU16;
 
-use super::ids::StepId;
-use super::ir::{CallIR, EffectIR, Instruction, Label, MatchIR, ReturnIR};
+use crate::bytecode::StepId;
+use crate::bytecode::ir::{CallIR, EffectIR, Instruction, Label, MatchIR, ReturnIR};
+use crate::bytecode::EffectOpcode;
+use crate::bytecode::Nav;
 use super::layout::CacheAligned;
-use crate::bytecode::effects::EffectOpcode;
-use crate::bytecode::nav::Nav;
 
 #[test]
 fn layout_empty() {
diff --git a/crates/plotnik-lib/src/query/codegen.rs b/crates/plotnik-lib/src/emit/mod.rs
similarity index 97%
rename from crates/plotnik-lib/src/query/codegen.rs
rename to crates/plotnik-lib/src/emit/mod.rs
index 3f6067a6..0cb3ccf5 100644
--- a/crates/plotnik-lib/src/query/codegen.rs
+++ b/crates/plotnik-lib/src/emit/mod.rs
@@ -1,6 +1,21 @@
-//! Bytecode emission from LinkedQuery.
+//! Bytecode emission from compiled queries.
 //!
-//! Converts the analyzed query representation into the binary bytecode format.
+//! Converts the compiled IR into the binary bytecode format. This module handles:
+//! - String table construction and interning
+//! - Type table building with field resolution
+//! - Cache-aligned instruction layout
+//! - Section assembly and header generation
+//!
+//! Entry points:
+//! - [`emit`]: Emit bytecode without language linking
+//! - [`emit_linked`]: Emit bytecode with node type/field validation
+
+pub mod layout;
+
+#[cfg(all(test, feature = "plotnik-langs"))]
+mod codegen_tests;
+#[cfg(test)]
+mod layout_tests;
 
 use std::collections::{HashMap, HashSet};
 
@@ -8,19 +23,19 @@ use indexmap::IndexMap;
 use plotnik_core::{Interner, NodeFieldId, NodeTypeId, Symbol};
 
 use crate::bytecode::ir::Label;
-use crate::bytecode::layout::CacheAligned;
 use crate::bytecode::{
     Entrypoint, FieldSymbol, Header, NodeSymbol, QTypeId, SECTION_ALIGN, StepId, StringId,
     TriviaEntry, TypeDef, TypeMember, TypeMetaHeader, TypeName,
 };
 use crate::type_system::TypeKind;
 
-use super::compile::Compiler;
-use super::query::LinkedQuery;
-use super::symbol_table::SymbolTable;
-use super::type_check::{
+use crate::compile::Compiler;
+use crate::query::query::LinkedQuery;
+use crate::analyze::symbol_table::SymbolTable;
+use crate::analyze::type_check::{
     FieldInfo, TYPE_NODE, TYPE_STRING, TYPE_VOID, TypeContext, TypeId, TypeShape,
 };
+use layout::CacheAligned;
 
 /// Error during bytecode emission.
 #[derive(Clone, Debug)]
@@ -40,7 +55,7 @@ pub enum EmitError {
     /// String not found in interner.
     StringNotFound(Symbol),
     /// Compilation error.
-    Compile(super::compile::CompileError),
+    Compile(crate::compile::CompileError),
 }
 
 impl std::fmt::Display for EmitError {
diff --git a/crates/plotnik-lib/src/lib.rs b/crates/plotnik-lib/src/lib.rs
index 91dfa05c..10c3e438 100644
--- a/crates/plotnik-lib/src/lib.rs
+++ b/crates/plotnik-lib/src/lib.rs
@@ -16,9 +16,12 @@
 
 #![cfg_attr(coverage_nightly, feature(coverage_attribute))]
 
+pub mod analyze;
 pub mod bytecode;
-pub mod codegen;
+pub mod typegen;
+pub mod compile;
 pub mod diagnostics;
+pub mod emit;
 pub mod parser;
 pub mod query;
 pub mod type_system;
diff --git a/crates/plotnik-lib/src/query/dump.rs b/crates/plotnik-lib/src/query/dump.rs
index 96aefadf..ed26222c 100644
--- a/crates/plotnik-lib/src/query/dump.rs
+++ b/crates/plotnik-lib/src/query/dump.rs
@@ -41,7 +41,7 @@ mod test_helpers {
             let bytecode = self.emit().expect("bytecode emission should succeed");
             let module = crate::bytecode::Module::from_bytes(bytecode)
                 .expect("module loading should succeed");
-            crate::bytecode::emit::emit_typescript(&module)
+            crate::typegen::typescript::emit(&module)
         }
     }
 }
diff --git a/crates/plotnik-lib/src/query/mod.rs b/crates/plotnik-lib/src/query/mod.rs
index 703da0cd..ccbe80a1 100644
--- a/crates/plotnik-lib/src/query/mod.rs
+++ b/crates/plotnik-lib/src/query/mod.rs
@@ -1,39 +1,18 @@
 mod dump;
-mod invariants;
 mod printer;
-mod refs;
-mod source_map;
-mod utils;
+pub mod source_map;
+
 pub use printer::QueryPrinter;
 pub use query::{Query, QueryBuilder};
 pub use source_map::{SourceId, SourceMap};
-pub use symbol_table::SymbolTable;
 
-pub mod alt_kinds;
-pub mod anchors;
-pub mod compile;
-mod dependencies;
-pub mod codegen;
-pub mod link;
 #[allow(clippy::module_inception)]
 pub mod query;
-pub mod symbol_table;
-pub mod type_check;
-pub mod visitor;
 
-#[cfg(test)]
-mod alt_kinds_tests;
-#[cfg(test)]
-mod anchors_tests;
-#[cfg(test)]
-mod dependencies_tests;
-#[cfg(all(test, feature = "plotnik-langs"))]
-mod codegen_tests;
-#[cfg(all(test, feature = "plotnik-langs"))]
-mod link_tests;
+// Re-export from analyze/ for backwards compatibility
+pub use crate::analyze::SymbolTable;
+
 #[cfg(test)]
 mod printer_tests;
 #[cfg(test)]
 mod query_tests;
-#[cfg(test)]
-mod symbol_table_tests;
diff --git a/crates/plotnik-lib/src/query/printer.rs b/crates/plotnik-lib/src/query/printer.rs
index 3386dee5..05fd0f69 100644
--- a/crates/plotnik-lib/src/query/printer.rs
+++ b/crates/plotnik-lib/src/query/printer.rs
@@ -9,7 +9,7 @@ use crate::parser::{self as ast, SyntaxNode};
 
 use super::Query;
 use super::source_map::SourceKind;
-use super::type_check::Arity;
+use crate::analyze::type_check::Arity;
 
 /// Returns indentation string for the given level.
 fn indent(level: usize) -> String {
@@ -167,7 +167,7 @@ impl<'q> QueryPrinter<'q> {
         visited.insert(name.to_string());
 
         if let Some(body) = self.query.symbol_table.get(name) {
-            let refs_set = super::refs::collect_ref_names(body);
+            let refs_set = crate::analyze::refs::collect_ref_names(body);
             let mut refs: Vec<_> = refs_set.iter().map(|s| s.as_str()).collect();
             refs.sort();
             for r in refs {
diff --git a/crates/plotnik-lib/src/query/query.rs b/crates/plotnik-lib/src/query/query.rs
index 15c0920c..8d96e981 100644
--- a/crates/plotnik-lib/src/query/query.rs
+++ b/crates/plotnik-lib/src/query/query.rs
@@ -6,14 +6,13 @@ use plotnik_core::{Interner, NodeFieldId, NodeTypeId, Symbol};
 use plotnik_langs::Lang;
 
 use crate::Diagnostics;
+use crate::analyze::dependencies;
+use crate::analyze::link;
+use crate::analyze::symbol_table::{SymbolTable, resolve_names};
+use crate::analyze::type_check::{self, Arity, TypeContext};
+use crate::analyze::validation::{validate_alt_kinds, validate_anchors};
 use crate::parser::{Parser, Root, SyntaxNode, lexer::lex};
-use crate::query::alt_kinds::validate_alt_kinds;
-use crate::query::anchors::validate_anchors;
-use crate::query::dependencies;
-use crate::query::link;
 use crate::query::source_map::{SourceId, SourceMap};
-use crate::query::symbol_table::{SymbolTable, resolve_names};
-use crate::query::type_check::{self, Arity, TypeContext};
 
 const DEFAULT_QUERY_PARSE_FUEL: u32 = 1_000_000;
 const DEFAULT_QUERY_PARSE_MAX_DEPTH: u32 = 4096;
@@ -203,11 +202,11 @@ impl QueryAnalyzed {
     /// Emit bytecode without language linking (no node type/field validation).
     ///
     /// Returns `Err(EmitError::InvalidQuery)` if the query has validation errors.
-    pub fn emit(&self) -> Result<Vec<u8>, super::codegen::EmitError> {
+    pub fn emit(&self) -> Result<Vec<u8>, crate::emit::EmitError> {
         if !self.is_valid() {
-            return Err(super::codegen::EmitError::InvalidQuery);
+            return Err(crate::emit::EmitError::InvalidQuery);
         }
-        super::codegen::emit(&self.type_context, &self.interner, &self.symbol_table)
+        crate::emit::emit(&self.type_context, &self.interner, &self.symbol_table)
     }
 
     pub fn link(mut self, lang: &Lang) -> LinkedQuery {
@@ -277,11 +276,11 @@ impl LinkedQuery {
     /// Emit bytecode with node type/field symbols from language linking.
     ///
     /// Returns `Err(EmitError::InvalidQuery)` if the query has validation errors.
-    pub fn emit(&self) -> Result<Vec<u8>, super::codegen::EmitError> {
+    pub fn emit(&self) -> Result<Vec<u8>, crate::emit::EmitError> {
         if !self.is_valid() {
-            return Err(super::codegen::EmitError::InvalidQuery);
+            return Err(crate::emit::EmitError::InvalidQuery);
         }
-        super::codegen::emit_linked(self)
+        crate::emit::emit_linked(self)
     }
 }
 
diff --git a/crates/plotnik-lib/src/query/query_tests.rs b/crates/plotnik-lib/src/query/query_tests.rs
index 2593b0df..bea5c1b6 100644
--- a/crates/plotnik-lib/src/query/query_tests.rs
+++ b/crates/plotnik-lib/src/query/query_tests.rs
@@ -94,7 +94,7 @@ impl QueryAnalyzed {
         // Emit to bytecode and then emit TypeScript from the bytecode module
         let bytecode = query.emit().expect("bytecode emission should succeed");
         let module = Module::from_bytes(bytecode).expect("module loading should succeed");
-        crate::bytecode::emit::emit_typescript(&module)
+        crate::typegen::typescript::emit(&module)
     }
 
     #[track_caller]
diff --git a/crates/plotnik-lib/src/typegen/mod.rs b/crates/plotnik-lib/src/typegen/mod.rs
new file mode 100644
index 00000000..5c94f6cf
--- /dev/null
+++ b/crates/plotnik-lib/src/typegen/mod.rs
@@ -0,0 +1,16 @@
+//! Type declaration generation from compiled bytecode.
+//!
+//! Extracts type metadata from bytecode modules and generates type declarations
+//! for target languages. Currently supports TypeScript `.d.ts` generation.
+//!
+//! # Example
+//!
+//! ```ignore
+//! use plotnik_lib::typegen::typescript;
+//! use plotnik_lib::bytecode::Module;
+//!
+//! let module = Module::from_bytes(bytecode)?;
+//! let output = typescript::emit(&module);
+//! ```
+
+pub mod typescript;
diff --git a/crates/plotnik-lib/src/codegen/typescript.rs b/crates/plotnik-lib/src/typegen/typescript.rs
similarity index 100%
rename from crates/plotnik-lib/src/codegen/typescript.rs
rename to crates/plotnik-lib/src/typegen/typescript.rs