diff --git a/docker-dev b/docker-dev
index a58f7617c..83aff9d5d 100755
--- a/docker-dev
+++ b/docker-dev
@@ -48,174 +48,6 @@ export COLORBT_SHOW_HIDDEN="0"
 export RUST_LOG="warn"
 export CARGO_BUILD_TARGET_DIR="${BUILD_DIR_REL}"
 
-export LINT_NORMAL="\
--Wfuture_incompatible \
--Wnonstandard_style \
--Wrust_2018_idioms \
--Wtrivial_numeric_casts \
-\
--Wclippy::all \
-\
--Wclippy::await_holding_lock \
--Wclippy::char_lit_as_u8 \
--Wclippy::checked_conversions \
--Wclippy::dbg_macro \
--Wclippy::debug_assert_with_mut_call \
--Wclippy::disallowed_script_idents \
--Wclippy::doc_markdown \
--Wclippy::empty_enum \
--Wclippy::enum_glob_use \
--Wclippy::equatable_if_let \
--Wclippy::exit \
--Wclippy::expl_impl_clone_on_copy \
--Wclippy::explicit_deref_methods \
--Wclippy::explicit_into_iter_loop \
--Wclippy::fallible_impl_from \
--Wclippy::filter_map_next \
--Wclippy::flat_map_option \
--Wclippy::float_cmp_const \
--Wclippy::fn_params_excessive_bools \
--Wclippy::fn_to_numeric_cast_any \
--Wclippy::from_iter_instead_of_collect \
--Wclippy::if_let_mutex \
--Wclippy::implicit_clone \
--Wclippy::imprecise_flops \
--Wclippy::index_refutable_slice \
--Wclippy::inefficient_to_string \
--Wclippy::invalid_upcast_comparisons \
--Wclippy::iter_not_returning_iterator \
--Wclippy::large_digit_groups \
--Wclippy::large_stack_arrays \
--Wclippy::large_types_passed_by_value \
--Wclippy::let_unit_value \
--Wclippy::linkedlist \
--Wclippy::lossy_float_literal \
--Wclippy::macro_use_imports \
--Wclippy::manual_ok_or \
--Wclippy::map_err_ignore \
--Wclippy::map_flatten \
--Wclippy::map_unwrap_or \
--Wclippy::match_on_vec_items \
--Wclippy::match_same_arms \
--Wclippy::match_wild_err_arm \
--Wclippy::match_wildcard_for_single_variants \
--Wclippy::mem_forget \
--Wclippy::mismatched_target_os \
--Wclippy::missing_enforced_import_renames \
--Wclippy::mut_mut \
--Wclippy::mutex_integer \
--Wclippy::needless_continue \
--Wclippy::needless_for_each \
--Wclippy::negative_feature_names \
--Wclippy::nonstandard_macro_braces \
--Wclippy::option_option \
--Wclippy::path_buf_push_overwrite \
--Wclippy::ptr_as_ptr \
--Wclippy::rc_mutex \
--Wclippy::ref_option_ref \
--Wclippy::rest_pat_in_fully_bound_structs \
--Wclippy::same_functions_in_if_condition \
--Wclippy::semicolon_if_nothing_returned \
--Wclippy::single_match_else \
--Wclippy::string_add \
--Wclippy::string_add_assign \
--Wclippy::string_lit_as_bytes \
--Wclippy::string_to_string \
--Wclippy::todo \
--Wclippy::trailing_empty_array \
--Wclippy::trait_duplication_in_bounds \
--Wclippy::unimplemented \
--Wclippy::unnecessary_wraps \
--Wclippy::unnested_or_patterns \
--Wclippy::useless_transmute \
--Wclippy::verbose_file_reads \
--Wclippy::zero_sized_map_values \
-"
-
-export LINT_EXTRA="\
-  ${LINT_NORMAL} \
-  -Wclippy::pedantic \
-"
-
-export LINT_CRAZY="\
-  ${LINT_EXTRA} \
-  -Wclippy::restriction \
-  -Wclippy::nursery \
-"
-
-export LINT_ALLOW_NOW_BUT_FIX_THESE_LATER=" \
--Aclippy::cognitive-complexity \
--Aclippy::else-if-without-else  \
--Aclippy::expect-used \
--Aclippy::missing-const-for-fn \
--Aclippy::panic \
--Aclippy::panic-in-result-fn \
--Aclippy::suboptimal_flops \
--Aclippy::too_many_arguments \
--Aclippy::unsafe-derive-deserialize \
--Aclippy::unwrap-in-result \
--Aclippy::unwrap-used \
--Aclippy::useless-transmute \
-"
-
-export LINT_ALLOW=" \
-${LINT_ALLOW_NOW_BUT_FIX_THESE_LATER} \
--Aclippy::as-conversions  \
--Aclippy::cast-lossless \
--Aclippy::cast-possible-truncation \
--Aclippy::cast-possible-wrap \
--Aclippy::cast-precision-loss \
--Aclippy::cast-sign-loss \
--Aclippy::default-numeric-fallback \
--Aclippy::doc-markdown \
--Aclippy::exhaustive-enums \
--Aclippy::exhaustive-structs \
--Aclippy::float-arithmetic \
--Aclippy::if-not-else \
--Aclippy::implicit-hasher \
--Aclippy::implicit-return  \
--Aclippy::inconsistent_digit_grouping \
--Aclippy::indexing-slicing \
--Aclippy::integer-arithmetic \
--Aclippy::integer-division \
--Aclippy::iter_nth_zero \
--Aclippy::large_digit_groups \
--Aclippy::let-underscore-must-use \
--Aclippy::match-same-arms \
--Aclippy::missing-docs-in-private-items  \
--Aclippy::missing-errors-doc \
--Aclippy::missing-panics-doc \
--Aclippy::missing_inline_in_public_items \
--Aclippy::mod-module-files \
--Aclippy::module-name-repetitions \
--Aclippy::module_inception \
--Aclippy::must-use-candidate \
--Aclippy::new_without_default \
--Aclippy::non-ascii-literal \
--Aclippy::option-if-let-else \
--Aclippy::pattern-type-mismatch \
--Aclippy::print-stderr  \
--Aclippy::print-stdout  \
--Aclippy::separated-literal-suffix \
--Aclippy::shadow-reuse \
--Aclippy::shadow-same \
--Aclippy::shadow-unrelated \
--Aclippy::should_implement_trait \
--Aclippy::similar-names \
--Aclippy::too-many-lines \
--Aclippy::unnecessary-wraps \
--Aclippy::unreachable \
--Aclippy::unreadable-literal  \
--Aclippy::unused-self \
--Aclippy::unused-unit \
--Aclippy::use-debug  \
--Aclippy::use-self \
--Aclippy::wildcard-enum-match-arm \
-"
-
-export LINT_FIX="--fix --allow-staged"
-
-
 export EXTENSIONS_TO_WATCH="rs,toml,lock"
 
 export FILES_TO_WATCH="\
@@ -240,6 +72,8 @@ export FILES_TO_IGNORE="\
 -i 'packages_rs/nextclade-web/src/gen/' \
 "
 
+export LINT_FIX="--fix --allow-staged"
+
 BUILD=0
 RUN=0
 WASM=0
diff --git a/packages_rs/nextclade-web/src/lib.rs b/packages_rs/nextclade-web/src/lib.rs
index 9fe005be0..94441389e 100644
--- a/packages_rs/nextclade-web/src/lib.rs
+++ b/packages_rs/nextclade-web/src/lib.rs
@@ -1,3 +1,168 @@
+// Configuration of Rust lints (static analysis). Scroll past it to find the actual code.
+// This needs to be kept in each root module right now, which is inconvenient and error-prone.
+// Hopefully it gets fixed soon. For a good summary see here: https://github.com/EmbarkStudios/rust-ecosystem/issues/59
+//
+//
+// Disable some of the default rust checks
+#![allow(dead_code)]
+#![allow(unused_imports)]
+#![allow(unused_variables)]
+//
+// Enable some of the default lints which are disabled by default
+#![warn(nonstandard_style)]
+#![warn(rust_2018_idioms)]
+#![warn(trivial_numeric_casts)]
+//
+// Enable all clippy lint groups
+// Order is important!
+#![warn(clippy::all)]
+#![warn(clippy::pedantic)]
+#![allow(clippy::blanket_clippy_restriction_lints)]
+#![warn(clippy::restriction)]
+#![warn(clippy::nursery)]
+//
+// Enable some of the clippy lints disabled by default
+#![warn(clippy::await_holding_lock)]
+#![warn(clippy::char_lit_as_u8)]
+#![warn(clippy::checked_conversions)]
+#![warn(clippy::dbg_macro)]
+#![warn(clippy::debug_assert_with_mut_call)]
+#![warn(clippy::disallowed_script_idents)]
+#![warn(clippy::doc_markdown)]
+#![warn(clippy::empty_enum)]
+#![warn(clippy::enum_glob_use)]
+#![warn(clippy::equatable_if_let)]
+#![warn(clippy::exit)]
+#![warn(clippy::expl_impl_clone_on_copy)]
+#![warn(clippy::explicit_deref_methods)]
+#![warn(clippy::explicit_into_iter_loop)]
+#![warn(clippy::fallible_impl_from)]
+#![warn(clippy::filter_map_next)]
+#![warn(clippy::flat_map_option)]
+#![warn(clippy::float_cmp_const)]
+#![warn(clippy::fn_params_excessive_bools)]
+#![warn(clippy::fn_to_numeric_cast_any)]
+#![warn(clippy::from_iter_instead_of_collect)]
+#![warn(clippy::if_let_mutex)]
+#![warn(clippy::implicit_clone)]
+#![warn(clippy::imprecise_flops)]
+#![warn(clippy::index_refutable_slice)]
+#![warn(clippy::inefficient_to_string)]
+#![warn(clippy::invalid_upcast_comparisons)]
+#![warn(clippy::iter_not_returning_iterator)]
+#![warn(clippy::large_digit_groups)]
+#![warn(clippy::large_stack_arrays)]
+#![warn(clippy::large_types_passed_by_value)]
+#![warn(clippy::let_unit_value)]
+#![warn(clippy::linkedlist)]
+#![warn(clippy::lossy_float_literal)]
+#![warn(clippy::macro_use_imports)]
+#![warn(clippy::manual_ok_or)]
+#![warn(clippy::map_err_ignore)]
+#![warn(clippy::map_flatten)]
+#![warn(clippy::map_unwrap_or)]
+#![warn(clippy::match_on_vec_items)]
+#![warn(clippy::match_same_arms)]
+#![warn(clippy::match_wild_err_arm)]
+#![warn(clippy::match_wildcard_for_single_variants)]
+#![warn(clippy::mem_forget)]
+#![warn(clippy::mismatched_target_os)]
+#![warn(clippy::missing_enforced_import_renames)]
+#![warn(clippy::mut_mut)]
+#![warn(clippy::mutex_integer)]
+#![warn(clippy::needless_continue)]
+#![warn(clippy::needless_for_each)]
+#![warn(clippy::negative_feature_names)]
+#![warn(clippy::nonstandard_macro_braces)]
+#![warn(clippy::option_option)]
+#![warn(clippy::path_buf_push_overwrite)]
+#![warn(clippy::ptr_as_ptr)]
+#![warn(clippy::rc_mutex)]
+#![warn(clippy::ref_option_ref)]
+#![warn(clippy::rest_pat_in_fully_bound_structs)]
+#![warn(clippy::same_functions_in_if_condition)]
+#![warn(clippy::semicolon_if_nothing_returned)]
+#![warn(clippy::single_match_else)]
+#![warn(clippy::string_add)]
+#![warn(clippy::string_add_assign)]
+#![warn(clippy::string_lit_as_bytes)]
+#![warn(clippy::string_to_string)]
+#![warn(clippy::trailing_empty_array)]
+#![warn(clippy::trait_duplication_in_bounds)]
+#![warn(clippy::unimplemented)]
+#![warn(clippy::unnecessary_wraps)]
+#![warn(clippy::unnested_or_patterns)]
+#![warn(clippy::useless_transmute)]
+#![warn(clippy::verbose_file_reads)]
+#![warn(clippy::zero_sized_map_values)]
+//
+// Disabled clippy lints, up for discussion
+#![allow(clippy::cognitive_complexity)]
+#![allow(clippy::else_if_without_else)]
+#![allow(clippy::expect_used)]
+#![allow(clippy::missing_const_for_fn)]
+#![allow(clippy::panic)]
+#![allow(clippy::panic_in_result_fn)]
+#![allow(clippy::suboptimal_flops)]
+#![allow(clippy::too_many_arguments)]
+#![allow(clippy::unsafe_derive_deserialize)]
+#![allow(clippy::unwrap_in_result)]
+#![allow(clippy::unwrap_used)]
+#![allow(clippy::useless_transmute)]
+//
+// Disabled clippy lints, permanent
+#![allow(clippy::as_conversions)]
+#![allow(clippy::cast_lossless)]
+#![allow(clippy::cast_possible_truncation)]
+#![allow(clippy::cast_possible_wrap)]
+#![allow(clippy::cast_precision_loss)]
+#![allow(clippy::cast_sign_loss)]
+#![allow(clippy::default_numeric_fallback)]
+#![allow(clippy::doc_markdown)]
+#![allow(clippy::exhaustive_enums)]
+#![allow(clippy::exhaustive_structs)]
+#![allow(clippy::float_arithmetic)]
+#![allow(clippy::if_not_else)]
+#![allow(clippy::implicit_hasher)]
+#![allow(clippy::implicit_return)]
+#![allow(clippy::inconsistent_digit_grouping)]
+#![allow(clippy::indexing_slicing)]
+#![allow(clippy::integer_arithmetic)]
+#![allow(clippy::integer_division)]
+#![allow(clippy::iter_nth_zero)]
+#![allow(clippy::large_digit_groups)]
+#![allow(clippy::let_underscore_must_use)]
+#![allow(clippy::match_same_arms)]
+#![allow(clippy::missing_docs_in_private_items)]
+#![allow(clippy::missing_errors_doc)]
+#![allow(clippy::missing_inline_in_public_items)]
+#![allow(clippy::missing_panics_doc)]
+#![allow(clippy::mod_module_files)]
+#![allow(clippy::module_inception)]
+#![allow(clippy::module_name_repetitions)]
+#![allow(clippy::must_use_candidate)]
+#![allow(clippy::new_without_default)]
+#![allow(clippy::non_ascii_literal)]
+#![allow(clippy::option_if_let_else)]
+#![allow(clippy::pattern_type_mismatch)]
+#![allow(clippy::print_stderr)]
+#![allow(clippy::print_stdout)]
+#![allow(clippy::separated_literal_suffix)]
+#![allow(clippy::shadow_reuse)]
+#![allow(clippy::shadow_same)]
+#![allow(clippy::shadow_unrelated)]
+#![allow(clippy::should_implement_trait)]
+#![allow(clippy::similar_names)]
+#![allow(clippy::too_many_lines)]
+#![allow(clippy::unnecessary_wraps)]
+#![allow(clippy::unreachable)]
+#![allow(clippy::unreadable_literal)]
+#![allow(clippy::unused_self)]
+#![allow(clippy::unused_unit)]
+#![allow(clippy::use_debug)]
+#![allow(clippy::use_self)]
+#![allow(clippy::wildcard_enum_match_arm)]
+
 use wasm_bindgen::prelude::*;
 
 use nextclade::analyze::analyze::{AnalysisInput, AnalysisResult, Nextclade, NextcladeParams};
diff --git a/packages_rs/nextclade/src/bin/nextalign.rs b/packages_rs/nextclade/src/bin/nextalign.rs
index aadfec9b5..ad41d70e4 100644
--- a/packages_rs/nextclade/src/bin/nextalign.rs
+++ b/packages_rs/nextclade/src/bin/nextalign.rs
@@ -1,3 +1,168 @@
+// Configuration of Rust lints (static analysis). Scroll past it to find the actual code.
+// This needs to be kept in each root module right now, which is inconvenient and error-prone.
+// Hopefully it gets fixed soon. For a good summary see here: https://github.com/EmbarkStudios/rust-ecosystem/issues/59
+//
+//
+// Disable some of the default rust checks
+#![allow(dead_code)]
+#![allow(unused_imports)]
+#![allow(unused_variables)]
+//
+// Enable some of the default lints which are disabled by default
+#![warn(nonstandard_style)]
+#![warn(rust_2018_idioms)]
+#![warn(trivial_numeric_casts)]
+//
+// Enable all clippy lint groups
+// Order is important!
+#![warn(clippy::all)]
+#![warn(clippy::pedantic)]
+#![allow(clippy::blanket_clippy_restriction_lints)]
+#![warn(clippy::restriction)]
+#![warn(clippy::nursery)]
+//
+// Enable some of the clippy lints disabled by default
+#![warn(clippy::await_holding_lock)]
+#![warn(clippy::char_lit_as_u8)]
+#![warn(clippy::checked_conversions)]
+#![warn(clippy::dbg_macro)]
+#![warn(clippy::debug_assert_with_mut_call)]
+#![warn(clippy::disallowed_script_idents)]
+#![warn(clippy::doc_markdown)]
+#![warn(clippy::empty_enum)]
+#![warn(clippy::enum_glob_use)]
+#![warn(clippy::equatable_if_let)]
+#![warn(clippy::exit)]
+#![warn(clippy::expl_impl_clone_on_copy)]
+#![warn(clippy::explicit_deref_methods)]
+#![warn(clippy::explicit_into_iter_loop)]
+#![warn(clippy::fallible_impl_from)]
+#![warn(clippy::filter_map_next)]
+#![warn(clippy::flat_map_option)]
+#![warn(clippy::float_cmp_const)]
+#![warn(clippy::fn_params_excessive_bools)]
+#![warn(clippy::fn_to_numeric_cast_any)]
+#![warn(clippy::from_iter_instead_of_collect)]
+#![warn(clippy::if_let_mutex)]
+#![warn(clippy::implicit_clone)]
+#![warn(clippy::imprecise_flops)]
+#![warn(clippy::index_refutable_slice)]
+#![warn(clippy::inefficient_to_string)]
+#![warn(clippy::invalid_upcast_comparisons)]
+#![warn(clippy::iter_not_returning_iterator)]
+#![warn(clippy::large_digit_groups)]
+#![warn(clippy::large_stack_arrays)]
+#![warn(clippy::large_types_passed_by_value)]
+#![warn(clippy::let_unit_value)]
+#![warn(clippy::linkedlist)]
+#![warn(clippy::lossy_float_literal)]
+#![warn(clippy::macro_use_imports)]
+#![warn(clippy::manual_ok_or)]
+#![warn(clippy::map_err_ignore)]
+#![warn(clippy::map_flatten)]
+#![warn(clippy::map_unwrap_or)]
+#![warn(clippy::match_on_vec_items)]
+#![warn(clippy::match_same_arms)]
+#![warn(clippy::match_wild_err_arm)]
+#![warn(clippy::match_wildcard_for_single_variants)]
+#![warn(clippy::mem_forget)]
+#![warn(clippy::mismatched_target_os)]
+#![warn(clippy::missing_enforced_import_renames)]
+#![warn(clippy::mut_mut)]
+#![warn(clippy::mutex_integer)]
+#![warn(clippy::needless_continue)]
+#![warn(clippy::needless_for_each)]
+#![warn(clippy::negative_feature_names)]
+#![warn(clippy::nonstandard_macro_braces)]
+#![warn(clippy::option_option)]
+#![warn(clippy::path_buf_push_overwrite)]
+#![warn(clippy::ptr_as_ptr)]
+#![warn(clippy::rc_mutex)]
+#![warn(clippy::ref_option_ref)]
+#![warn(clippy::rest_pat_in_fully_bound_structs)]
+#![warn(clippy::same_functions_in_if_condition)]
+#![warn(clippy::semicolon_if_nothing_returned)]
+#![warn(clippy::single_match_else)]
+#![warn(clippy::string_add)]
+#![warn(clippy::string_add_assign)]
+#![warn(clippy::string_lit_as_bytes)]
+#![warn(clippy::string_to_string)]
+#![warn(clippy::trailing_empty_array)]
+#![warn(clippy::trait_duplication_in_bounds)]
+#![warn(clippy::unimplemented)]
+#![warn(clippy::unnecessary_wraps)]
+#![warn(clippy::unnested_or_patterns)]
+#![warn(clippy::useless_transmute)]
+#![warn(clippy::verbose_file_reads)]
+#![warn(clippy::zero_sized_map_values)]
+//
+// Disabled clippy lints, up for discussion
+#![allow(clippy::cognitive_complexity)]
+#![allow(clippy::else_if_without_else)]
+#![allow(clippy::expect_used)]
+#![allow(clippy::missing_const_for_fn)]
+#![allow(clippy::panic)]
+#![allow(clippy::panic_in_result_fn)]
+#![allow(clippy::suboptimal_flops)]
+#![allow(clippy::too_many_arguments)]
+#![allow(clippy::unsafe_derive_deserialize)]
+#![allow(clippy::unwrap_in_result)]
+#![allow(clippy::unwrap_used)]
+#![allow(clippy::useless_transmute)]
+//
+// Disabled clippy lints, permanent
+#![allow(clippy::as_conversions)]
+#![allow(clippy::cast_lossless)]
+#![allow(clippy::cast_possible_truncation)]
+#![allow(clippy::cast_possible_wrap)]
+#![allow(clippy::cast_precision_loss)]
+#![allow(clippy::cast_sign_loss)]
+#![allow(clippy::default_numeric_fallback)]
+#![allow(clippy::doc_markdown)]
+#![allow(clippy::exhaustive_enums)]
+#![allow(clippy::exhaustive_structs)]
+#![allow(clippy::float_arithmetic)]
+#![allow(clippy::if_not_else)]
+#![allow(clippy::implicit_hasher)]
+#![allow(clippy::implicit_return)]
+#![allow(clippy::inconsistent_digit_grouping)]
+#![allow(clippy::indexing_slicing)]
+#![allow(clippy::integer_arithmetic)]
+#![allow(clippy::integer_division)]
+#![allow(clippy::iter_nth_zero)]
+#![allow(clippy::large_digit_groups)]
+#![allow(clippy::let_underscore_must_use)]
+#![allow(clippy::match_same_arms)]
+#![allow(clippy::missing_docs_in_private_items)]
+#![allow(clippy::missing_errors_doc)]
+#![allow(clippy::missing_inline_in_public_items)]
+#![allow(clippy::missing_panics_doc)]
+#![allow(clippy::mod_module_files)]
+#![allow(clippy::module_inception)]
+#![allow(clippy::module_name_repetitions)]
+#![allow(clippy::must_use_candidate)]
+#![allow(clippy::new_without_default)]
+#![allow(clippy::non_ascii_literal)]
+#![allow(clippy::option_if_let_else)]
+#![allow(clippy::pattern_type_mismatch)]
+#![allow(clippy::print_stderr)]
+#![allow(clippy::print_stdout)]
+#![allow(clippy::separated_literal_suffix)]
+#![allow(clippy::shadow_reuse)]
+#![allow(clippy::shadow_same)]
+#![allow(clippy::shadow_unrelated)]
+#![allow(clippy::should_implement_trait)]
+#![allow(clippy::similar_names)]
+#![allow(clippy::too_many_lines)]
+#![allow(clippy::unnecessary_wraps)]
+#![allow(clippy::unreachable)]
+#![allow(clippy::unreadable_literal)]
+#![allow(clippy::unused_self)]
+#![allow(clippy::unused_unit)]
+#![allow(clippy::use_debug)]
+#![allow(clippy::use_self)]
+#![allow(clippy::wildcard_enum_match_arm)]
+
 use ctor::ctor;
 use eyre::Report;
 use nextclade::cli::nextalign_cli::{nextalign_parse_cli_args, NextalignCommands};
diff --git a/packages_rs/nextclade/src/bin/nextclade.rs b/packages_rs/nextclade/src/bin/nextclade.rs
index ea47d2fd2..67109dab0 100644
--- a/packages_rs/nextclade/src/bin/nextclade.rs
+++ b/packages_rs/nextclade/src/bin/nextclade.rs
@@ -1,3 +1,168 @@
+// Configuration of Rust lints (static analysis). Scroll past it to find the actual code.
+// This needs to be kept in each root module right now, which is inconvenient and error-prone.
+// Hopefully it gets fixed soon. For a good summary see here: https://github.com/EmbarkStudios/rust-ecosystem/issues/59
+//
+//
+// Disable some of the default rust checks
+#![allow(dead_code)]
+#![allow(unused_imports)]
+#![allow(unused_variables)]
+//
+// Enable some of the default lints which are disabled by default
+#![warn(nonstandard_style)]
+#![warn(rust_2018_idioms)]
+#![warn(trivial_numeric_casts)]
+//
+// Enable all clippy lint groups
+// Order is important!
+#![warn(clippy::all)]
+#![warn(clippy::pedantic)]
+#![allow(clippy::blanket_clippy_restriction_lints)]
+#![warn(clippy::restriction)]
+#![warn(clippy::nursery)]
+//
+// Enable some of the clippy lints disabled by default
+#![warn(clippy::await_holding_lock)]
+#![warn(clippy::char_lit_as_u8)]
+#![warn(clippy::checked_conversions)]
+#![warn(clippy::dbg_macro)]
+#![warn(clippy::debug_assert_with_mut_call)]
+#![warn(clippy::disallowed_script_idents)]
+#![warn(clippy::doc_markdown)]
+#![warn(clippy::empty_enum)]
+#![warn(clippy::enum_glob_use)]
+#![warn(clippy::equatable_if_let)]
+#![warn(clippy::exit)]
+#![warn(clippy::expl_impl_clone_on_copy)]
+#![warn(clippy::explicit_deref_methods)]
+#![warn(clippy::explicit_into_iter_loop)]
+#![warn(clippy::fallible_impl_from)]
+#![warn(clippy::filter_map_next)]
+#![warn(clippy::flat_map_option)]
+#![warn(clippy::float_cmp_const)]
+#![warn(clippy::fn_params_excessive_bools)]
+#![warn(clippy::fn_to_numeric_cast_any)]
+#![warn(clippy::from_iter_instead_of_collect)]
+#![warn(clippy::if_let_mutex)]
+#![warn(clippy::implicit_clone)]
+#![warn(clippy::imprecise_flops)]
+#![warn(clippy::index_refutable_slice)]
+#![warn(clippy::inefficient_to_string)]
+#![warn(clippy::invalid_upcast_comparisons)]
+#![warn(clippy::iter_not_returning_iterator)]
+#![warn(clippy::large_digit_groups)]
+#![warn(clippy::large_stack_arrays)]
+#![warn(clippy::large_types_passed_by_value)]
+#![warn(clippy::let_unit_value)]
+#![warn(clippy::linkedlist)]
+#![warn(clippy::lossy_float_literal)]
+#![warn(clippy::macro_use_imports)]
+#![warn(clippy::manual_ok_or)]
+#![warn(clippy::map_err_ignore)]
+#![warn(clippy::map_flatten)]
+#![warn(clippy::map_unwrap_or)]
+#![warn(clippy::match_on_vec_items)]
+#![warn(clippy::match_same_arms)]
+#![warn(clippy::match_wild_err_arm)]
+#![warn(clippy::match_wildcard_for_single_variants)]
+#![warn(clippy::mem_forget)]
+#![warn(clippy::mismatched_target_os)]
+#![warn(clippy::missing_enforced_import_renames)]
+#![warn(clippy::mut_mut)]
+#![warn(clippy::mutex_integer)]
+#![warn(clippy::needless_continue)]
+#![warn(clippy::needless_for_each)]
+#![warn(clippy::negative_feature_names)]
+#![warn(clippy::nonstandard_macro_braces)]
+#![warn(clippy::option_option)]
+#![warn(clippy::path_buf_push_overwrite)]
+#![warn(clippy::ptr_as_ptr)]
+#![warn(clippy::rc_mutex)]
+#![warn(clippy::ref_option_ref)]
+#![warn(clippy::rest_pat_in_fully_bound_structs)]
+#![warn(clippy::same_functions_in_if_condition)]
+#![warn(clippy::semicolon_if_nothing_returned)]
+#![warn(clippy::single_match_else)]
+#![warn(clippy::string_add)]
+#![warn(clippy::string_add_assign)]
+#![warn(clippy::string_lit_as_bytes)]
+#![warn(clippy::string_to_string)]
+#![warn(clippy::trailing_empty_array)]
+#![warn(clippy::trait_duplication_in_bounds)]
+#![warn(clippy::unimplemented)]
+#![warn(clippy::unnecessary_wraps)]
+#![warn(clippy::unnested_or_patterns)]
+#![warn(clippy::useless_transmute)]
+#![warn(clippy::verbose_file_reads)]
+#![warn(clippy::zero_sized_map_values)]
+//
+// Disabled clippy lints, up for discussion
+#![allow(clippy::cognitive_complexity)]
+#![allow(clippy::else_if_without_else)]
+#![allow(clippy::expect_used)]
+#![allow(clippy::missing_const_for_fn)]
+#![allow(clippy::panic)]
+#![allow(clippy::panic_in_result_fn)]
+#![allow(clippy::suboptimal_flops)]
+#![allow(clippy::too_many_arguments)]
+#![allow(clippy::unsafe_derive_deserialize)]
+#![allow(clippy::unwrap_in_result)]
+#![allow(clippy::unwrap_used)]
+#![allow(clippy::useless_transmute)]
+//
+// Disabled clippy lints, permanent
+#![allow(clippy::as_conversions)]
+#![allow(clippy::cast_lossless)]
+#![allow(clippy::cast_possible_truncation)]
+#![allow(clippy::cast_possible_wrap)]
+#![allow(clippy::cast_precision_loss)]
+#![allow(clippy::cast_sign_loss)]
+#![allow(clippy::default_numeric_fallback)]
+#![allow(clippy::doc_markdown)]
+#![allow(clippy::exhaustive_enums)]
+#![allow(clippy::exhaustive_structs)]
+#![allow(clippy::float_arithmetic)]
+#![allow(clippy::if_not_else)]
+#![allow(clippy::implicit_hasher)]
+#![allow(clippy::implicit_return)]
+#![allow(clippy::inconsistent_digit_grouping)]
+#![allow(clippy::indexing_slicing)]
+#![allow(clippy::integer_arithmetic)]
+#![allow(clippy::integer_division)]
+#![allow(clippy::iter_nth_zero)]
+#![allow(clippy::large_digit_groups)]
+#![allow(clippy::let_underscore_must_use)]
+#![allow(clippy::match_same_arms)]
+#![allow(clippy::missing_docs_in_private_items)]
+#![allow(clippy::missing_errors_doc)]
+#![allow(clippy::missing_inline_in_public_items)]
+#![allow(clippy::missing_panics_doc)]
+#![allow(clippy::mod_module_files)]
+#![allow(clippy::module_inception)]
+#![allow(clippy::module_name_repetitions)]
+#![allow(clippy::must_use_candidate)]
+#![allow(clippy::new_without_default)]
+#![allow(clippy::non_ascii_literal)]
+#![allow(clippy::option_if_let_else)]
+#![allow(clippy::pattern_type_mismatch)]
+#![allow(clippy::print_stderr)]
+#![allow(clippy::print_stdout)]
+#![allow(clippy::separated_literal_suffix)]
+#![allow(clippy::shadow_reuse)]
+#![allow(clippy::shadow_same)]
+#![allow(clippy::shadow_unrelated)]
+#![allow(clippy::should_implement_trait)]
+#![allow(clippy::similar_names)]
+#![allow(clippy::too_many_lines)]
+#![allow(clippy::unnecessary_wraps)]
+#![allow(clippy::unreachable)]
+#![allow(clippy::unreadable_literal)]
+#![allow(clippy::unused_self)]
+#![allow(clippy::unused_unit)]
+#![allow(clippy::use_debug)]
+#![allow(clippy::use_self)]
+#![allow(clippy::wildcard_enum_match_arm)]
+
 use ctor::ctor;
 use eyre::Report;
 use nextclade::cli::nextclade_cli::{nextclade_parse_cli_args, NextcladeCommands};
diff --git a/packages_rs/nextclade/src/lib.rs b/packages_rs/nextclade/src/lib.rs
index 5c1d9c236..f0844c16f 100644
--- a/packages_rs/nextclade/src/lib.rs
+++ b/packages_rs/nextclade/src/lib.rs
@@ -1,3 +1,168 @@
+// Configuration of Rust lints (static analysis). Scroll past it to find the actual code.
+// This needs to be kept in each root module right now, which is inconvenient and error-prone.
+// Hopefully it gets fixed soon. For a good summary see here: https://github.com/EmbarkStudios/rust-ecosystem/issues/59
+//
+//
+// Disable some of the default rust checks
+#![allow(dead_code)]
+#![allow(unused_imports)]
+#![allow(unused_variables)]
+//
+// Enable some of the default lints which are disabled by default
+#![warn(nonstandard_style)]
+#![warn(rust_2018_idioms)]
+#![warn(trivial_numeric_casts)]
+//
+// Enable all clippy lint groups
+// Order is important!
+#![warn(clippy::all)]
+#![warn(clippy::pedantic)]
+#![allow(clippy::blanket_clippy_restriction_lints)]
+#![warn(clippy::restriction)]
+#![warn(clippy::nursery)]
+//
+// Enable some of the clippy lints disabled by default
+#![warn(clippy::await_holding_lock)]
+#![warn(clippy::char_lit_as_u8)]
+#![warn(clippy::checked_conversions)]
+#![warn(clippy::dbg_macro)]
+#![warn(clippy::debug_assert_with_mut_call)]
+#![warn(clippy::disallowed_script_idents)]
+#![warn(clippy::doc_markdown)]
+#![warn(clippy::empty_enum)]
+#![warn(clippy::enum_glob_use)]
+#![warn(clippy::equatable_if_let)]
+#![warn(clippy::exit)]
+#![warn(clippy::expl_impl_clone_on_copy)]
+#![warn(clippy::explicit_deref_methods)]
+#![warn(clippy::explicit_into_iter_loop)]
+#![warn(clippy::fallible_impl_from)]
+#![warn(clippy::filter_map_next)]
+#![warn(clippy::flat_map_option)]
+#![warn(clippy::float_cmp_const)]
+#![warn(clippy::fn_params_excessive_bools)]
+#![warn(clippy::fn_to_numeric_cast_any)]
+#![warn(clippy::from_iter_instead_of_collect)]
+#![warn(clippy::if_let_mutex)]
+#![warn(clippy::implicit_clone)]
+#![warn(clippy::imprecise_flops)]
+#![warn(clippy::index_refutable_slice)]
+#![warn(clippy::inefficient_to_string)]
+#![warn(clippy::invalid_upcast_comparisons)]
+#![warn(clippy::iter_not_returning_iterator)]
+#![warn(clippy::large_digit_groups)]
+#![warn(clippy::large_stack_arrays)]
+#![warn(clippy::large_types_passed_by_value)]
+#![warn(clippy::let_unit_value)]
+#![warn(clippy::linkedlist)]
+#![warn(clippy::lossy_float_literal)]
+#![warn(clippy::macro_use_imports)]
+#![warn(clippy::manual_ok_or)]
+#![warn(clippy::map_err_ignore)]
+#![warn(clippy::map_flatten)]
+#![warn(clippy::map_unwrap_or)]
+#![warn(clippy::match_on_vec_items)]
+#![warn(clippy::match_same_arms)]
+#![warn(clippy::match_wild_err_arm)]
+#![warn(clippy::match_wildcard_for_single_variants)]
+#![warn(clippy::mem_forget)]
+#![warn(clippy::mismatched_target_os)]
+#![warn(clippy::missing_enforced_import_renames)]
+#![warn(clippy::mut_mut)]
+#![warn(clippy::mutex_integer)]
+#![warn(clippy::needless_continue)]
+#![warn(clippy::needless_for_each)]
+#![warn(clippy::negative_feature_names)]
+#![warn(clippy::nonstandard_macro_braces)]
+#![warn(clippy::option_option)]
+#![warn(clippy::path_buf_push_overwrite)]
+#![warn(clippy::ptr_as_ptr)]
+#![warn(clippy::rc_mutex)]
+#![warn(clippy::ref_option_ref)]
+#![warn(clippy::rest_pat_in_fully_bound_structs)]
+#![warn(clippy::same_functions_in_if_condition)]
+#![warn(clippy::semicolon_if_nothing_returned)]
+#![warn(clippy::single_match_else)]
+#![warn(clippy::string_add)]
+#![warn(clippy::string_add_assign)]
+#![warn(clippy::string_lit_as_bytes)]
+#![warn(clippy::string_to_string)]
+#![warn(clippy::trailing_empty_array)]
+#![warn(clippy::trait_duplication_in_bounds)]
+#![warn(clippy::unimplemented)]
+#![warn(clippy::unnecessary_wraps)]
+#![warn(clippy::unnested_or_patterns)]
+#![warn(clippy::useless_transmute)]
+#![warn(clippy::verbose_file_reads)]
+#![warn(clippy::zero_sized_map_values)]
+//
+// Disabled clippy lints, up for discussion
+#![allow(clippy::cognitive_complexity)]
+#![allow(clippy::else_if_without_else)]
+#![allow(clippy::expect_used)]
+#![allow(clippy::missing_const_for_fn)]
+#![allow(clippy::panic)]
+#![allow(clippy::panic_in_result_fn)]
+#![allow(clippy::suboptimal_flops)]
+#![allow(clippy::too_many_arguments)]
+#![allow(clippy::unsafe_derive_deserialize)]
+#![allow(clippy::unwrap_in_result)]
+#![allow(clippy::unwrap_used)]
+#![allow(clippy::useless_transmute)]
+//
+// Disabled clippy lints, permanent
+#![allow(clippy::as_conversions)]
+#![allow(clippy::cast_lossless)]
+#![allow(clippy::cast_possible_truncation)]
+#![allow(clippy::cast_possible_wrap)]
+#![allow(clippy::cast_precision_loss)]
+#![allow(clippy::cast_sign_loss)]
+#![allow(clippy::default_numeric_fallback)]
+#![allow(clippy::doc_markdown)]
+#![allow(clippy::exhaustive_enums)]
+#![allow(clippy::exhaustive_structs)]
+#![allow(clippy::float_arithmetic)]
+#![allow(clippy::if_not_else)]
+#![allow(clippy::implicit_hasher)]
+#![allow(clippy::implicit_return)]
+#![allow(clippy::inconsistent_digit_grouping)]
+#![allow(clippy::indexing_slicing)]
+#![allow(clippy::integer_arithmetic)]
+#![allow(clippy::integer_division)]
+#![allow(clippy::iter_nth_zero)]
+#![allow(clippy::large_digit_groups)]
+#![allow(clippy::let_underscore_must_use)]
+#![allow(clippy::match_same_arms)]
+#![allow(clippy::missing_docs_in_private_items)]
+#![allow(clippy::missing_errors_doc)]
+#![allow(clippy::missing_inline_in_public_items)]
+#![allow(clippy::missing_panics_doc)]
+#![allow(clippy::mod_module_files)]
+#![allow(clippy::module_inception)]
+#![allow(clippy::module_name_repetitions)]
+#![allow(clippy::must_use_candidate)]
+#![allow(clippy::new_without_default)]
+#![allow(clippy::non_ascii_literal)]
+#![allow(clippy::option_if_let_else)]
+#![allow(clippy::pattern_type_mismatch)]
+#![allow(clippy::print_stderr)]
+#![allow(clippy::print_stdout)]
+#![allow(clippy::separated_literal_suffix)]
+#![allow(clippy::shadow_reuse)]
+#![allow(clippy::shadow_same)]
+#![allow(clippy::shadow_unrelated)]
+#![allow(clippy::should_implement_trait)]
+#![allow(clippy::similar_names)]
+#![allow(clippy::too_many_lines)]
+#![allow(clippy::unnecessary_wraps)]
+#![allow(clippy::unreachable)]
+#![allow(clippy::unreadable_literal)]
+#![allow(clippy::unused_self)]
+#![allow(clippy::unused_unit)]
+#![allow(clippy::use_debug)]
+#![allow(clippy::use_self)]
+#![allow(clippy::wildcard_enum_match_arm)]
+
 pub mod align;
 pub mod analyze;
 pub mod cli;