diff --git a/Cargo.lock b/Cargo.lock
index b74eb36e..b44c8d3d 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -1558,12 +1558,9 @@ name = "quonlint"
 version = "0.2.0"
 dependencies = [
  "ariadne",
- "backend",
  "frontend",
  "glob",
  "insta",
- "melior",
- "mlir_bridge",
  "quon_core",
  "rayon",
  "serde",
diff --git a/Justfile b/Justfile
index a807d8d5..c7d0290d 100644
--- a/Justfile
+++ b/Justfile
@@ -148,6 +148,10 @@ ci-rust: setup-python
     cargo clippy --workspace {{WORKSPACE_EXCLUDE}} --all-targets -- -D warnings
     cargo build --release --workspace {{WORKSPACE_EXCLUDE}}
     cargo build --examples --workspace {{WORKSPACE_EXCLUDE}}
+    # MLIR-free module-seam feature combinations (issue #407). Runs after
+    # the release workspace build so `cargo build --release -p quonc` is a
+    # cache hit and the dev-profile MLIR-free builds reuse clippy's deps.
+    just ci-feature-seams
     export PATH="$PWD/.venv/bin:$PATH"
     export QUON_REQUIRE_LIT=1
     cargo nextest run --workspace {{WORKSPACE_EXCLUDE}}
@@ -209,6 +213,24 @@ na-rap-sweep:
       --csv /tmp/quon_na_rap_sweep/rap_table_i_sweep.csv
     echo "wrote /tmp/quon_na_rap_sweep/rap_table_i_sweep.csv"
 
+# Feature-combination module-seam checks (issue #407). Verifies the
+# MLIR-free seams stay MLIR-free: parser-only, analysis-only, and the
+# MLIR-free neutral-atom library build without linking LLVM/MLIR, while the
+# full compiler combination (quonc with frontend `full` + quon_na `mlir`)
+# still builds. Run inside `ci-rust` so the `--release -p quonc` line reuses
+# the release workspace build above as a cache hit.
+ci-feature-seams:
+    #!/usr/bin/env bash
+    set -euo pipefail
+    echo "==> frontend parser-only (no MLIR)"
+    cargo build -p frontend --no-default-features
+    echo "==> frontend analysis-only (no MLIR)"
+    cargo build -p frontend --no-default-features --features analyze
+    echo "==> quon_na MLIR-free (no LLVM/MLIR)"
+    cargo build -p quon_na --no-default-features
+    echo "==> quonc full compiler (frontend full + quon_na mlir)"
+    cargo build --release -p quonc
+
 # quonfmt · quonlint · LSP smoke on CI corpus
 ci-tooling: _tooling-build
     #!/usr/bin/env bash
diff --git a/docs/agents/validation.md b/docs/agents/validation.md
index 8576d727..7c8402c8 100644
--- a/docs/agents/validation.md
+++ b/docs/agents/validation.md
@@ -14,7 +14,7 @@ Static analysis and refinement-type checks for the Quon workspace.
 | `just test-fast` | `cargo test --workspace --exclude flux_verify` (lit soft-skips if tools missing; no Aer) |
 | `just test-ci` | Local CI parity: `ci-rust` + `ci-tooling` + `ci-docs-assert` (not the website build) |
 | `just ci-rust` | What the `ci.yml` `rust` job runs (sets `QUON_REQUIRE_LIT`); its `cargo test --workspace` step already includes the sample corpus catalog lint (`quonc/tests/samples_catalog.rs`, ADR-0025 / #185) as an ordinary workspace test crate |
-| `just ci-samples` | Local-only convenience: re-run just the sample corpus catalog lint (schema, paths, category coverage, README sections, `ci: smoke` typecheck) in isolation. **Not** part of `test-ci` or `ci.yml` — it would double-pay for what `ci-rust` already covers |
+| `just ci-feature-seams` | Invoked inside `just ci-rust` (#407): builds frontend parser-only, frontend analysis-only, `quon_na` MLIR-free (no LLVM/MLIR link), and the full-compiler `quonc` combination to keep the MLIR-free module seams intact |
 | `just ci-tooling` | What the `ci.yml` `tooling` job runs |
 | `just tooling-full` | Broader local fmt/lint corpus (not CI) |
 | `just qec-benchmarks-smoke` | #254 local convenience: one-cell ablation + nested Sinter (`--mode smoke`). CI smoke is the unittest in `just ci-rust`. |
diff --git a/frontend/Cargo.toml b/frontend/Cargo.toml
index a9b44db3..8f128036 100644
--- a/frontend/Cargo.toml
+++ b/frontend/Cargo.toml
@@ -14,8 +14,10 @@ default = ["full"]
 # is buildable and testable without linking LLVM/MLIR (ADR-0038, issue #206).
 analyze = ["dep:quon_core", "dep:z3"]
 # `full`: the whole frontend including the `lower` → `quantum.circ` MLIR adapter,
-# which pulls in `mlir_bridge` / `melior`. `quonc` / `quon_lsp` take this by
-# default; `quonfmt` uses `default-features = false` (parser only).
+# which pulls in `mlir_bridge` / `melior`. Only the compiler binary (`quonc`)
+# opts into this; `quonfmt` (parser only), `quonlint`, and `quon_lsp`
+# (analysis only) all use `default-features = false` so they never link
+# LLVM/MLIR (ADR-0038, issue #407).
 full = ["analyze", "dep:mlir_bridge", "dep:melior", "dep:anyhow"]
 
 [dependencies]
diff --git a/frontend/src/lib.rs b/frontend/src/lib.rs
index bbfb41a6..44442e73 100644
--- a/frontend/src/lib.rs
+++ b/frontend/src/lib.rs
@@ -23,11 +23,11 @@ pub mod pretty;
 // specialize) gates on `analyze`, which pulls in only `quon_core` / `z3` — no
 // `mlir_bridge` / `melior`. `specialized_circuit` (issue #206) is the typed
 // boundary between `elaborate` and `lower`. `lower` — the `quantum.circ` MLIR
-// adapter — is the only module that needs `full` (Melior). Cargo unifies
-// features across the workspace, so `quonfmt`'s `default-features = false`
-// (parser only) never strips these from `quon_lsp` / `quonc` (`full`), and
-// specialization is buildable/testable under `--features analyze` without
-// linking LLVM/MLIR.
+// adapter — is the only module that needs `full` (Melior). Only `quonc` opts
+// into `full`; `quonfmt` (parser only), `quonlint`, and `quon_lsp` (analysis
+// only) all use `default-features = false` so a tooling build never links
+// LLVM/MLIR, and specialization is buildable/testable under `--features
+// analyze` without linking LLVM/MLIR (ADR-0038, issue #407).
 #[cfg(feature = "analyze")]
 pub mod analysis;
 #[cfg(feature = "analyze")]
diff --git a/quon_lsp/Cargo.toml b/quon_lsp/Cargo.toml
index 721f7919..125923da 100644
--- a/quon_lsp/Cargo.toml
+++ b/quon_lsp/Cargo.toml
@@ -11,7 +11,7 @@ name = "quon_lsp"
 path = "src/main.rs"
 
 [dependencies]
-frontend           = { path = "../frontend" }
+frontend           = { path = "../frontend", default-features = false, features = ["analyze"] }
 quonfmt            = { path = "../quonfmt" }
 quonlint           = { path = "../quonlint" }
 tower-lsp          = { workspace = true }
diff --git a/quon_na/Cargo.toml b/quon_na/Cargo.toml
index e21b3844..b8c60908 100644
--- a/quon_na/Cargo.toml
+++ b/quon_na/Cargo.toml
@@ -8,7 +8,7 @@ repository.workspace = true
 description = "MLIR-free neutral-atom layout, schedule, and reporting types for Quon"
 
 [features]
-default = ["mlir"]
+default = []
 # Opt-in Flux refinement-type checking. Off by default so the stable workspace
 # build never compiles `flux-rs`; enabled by `cargo flux -p quon_na
 # --no-default-features --features flux` (nightly).
diff --git a/quonc/Cargo.toml b/quonc/Cargo.toml
index 5f70d62f..530795b3 100644
--- a/quonc/Cargo.toml
+++ b/quonc/Cargo.toml
@@ -23,11 +23,11 @@ default = []
 solver = ["quon_na/solver"]
 
 [dependencies]
-frontend    = { path = "../frontend" }
+frontend    = { path = "../frontend", default-features = false, features = ["full"] }
 mlir_bridge = { path = "../mlir_bridge" }
 backend     = { path = "../backend" }
 quon_core   = { path = "../quon_core" }
-quon_na     = { path = "../quon_na" }
+quon_na     = { path = "../quon_na", default-features = false, features = ["mlir"] }
 quon_qec    = { path = "../quon_qec" }
 melior      = { workspace = true }
 clap        = { workspace = true }
diff --git a/quonlint/Cargo.toml b/quonlint/Cargo.toml
index 248b9f64..383f0cb5 100644
--- a/quonlint/Cargo.toml
+++ b/quonlint/Cargo.toml
@@ -8,14 +8,14 @@ repository.workspace = true
 
 [features]
 default = []
-ir-analysis = ["dep:mlir_bridge", "dep:melior", "dep:backend"]
+# quonlint only needs the Melior-free analysis pipeline (parse → desugar →
+# typecheck → elaborate). IR/lowering rules are out of scope here; the
+# `frontend` `analyze` feature pulls in `quon_core` / `z3` only — no
+# `mlir_bridge` / `melior` (ADR-0038, issue #407).
 
 [dependencies]
-frontend    = { path = "../frontend" }
+frontend    = { path = "../frontend", default-features = false, features = ["analyze"] }
 quon_core   = { path = "../quon_core" }
-backend     = { path = "../backend", optional = true }
-mlir_bridge = { path = "../mlir_bridge", optional = true }
-melior      = { workspace = true, optional = true }
 thiserror   = { workspace = true }
 serde       = { workspace = true, features = ["derive"] }
 serde_json  = { workspace = true }