fraiseql-cli 2.19.1

//! Schema merger - combines language-generated types.json with TOML configuration
//!
//! This module merges:
//! - types.json: Generated by language implementations (Python, Go, etc.)
//! - fraiseql.toml: Configuration (security, federation, observers, caching, etc.)
//!
//! Result: Complete `IntermediateSchema` ready for compilation

use std::fs;

use anyhow::{Context, Result};
use fraiseql_core::schema::CrudNamingConfig;
use serde_json::{Value, json};

use crate::{
    config::TomlSchema,
    schema::{
        IntermediateSchema,
        intermediate::{IntermediateArgument, IntermediateQueryDefaults},
    },
};

/// Convert a PascalCase GraphQL type name to a `snake_case` entity name.
///
/// Used to derive the entity segment for CRUD naming templates:
/// `"UserProfile"` → `"user_profile"`, `"User"` → `"user"`.
pub(crate) fn pascal_to_snake(type_name: &str) -> String {
    let mut out = String::with_capacity(type_name.len() + 4);
    for (i, ch) in type_name.chars().enumerate() {
        if ch.is_uppercase() && i > 0 {
            out.push('_');
        }
        out.push(ch.to_ascii_lowercase());
    }
    out
}

/// Resolve the `sql_source` for a TOML-defined mutation.
///
/// Precedence (highest first):
/// 1. Explicit `sql_source` on the mutation.
/// 2. `[crud]` naming config resolved from `operation` + entity derived from `return_type`.
///
/// Returns an error when neither is available, naming the offending mutation.
fn resolve_mutation_sql_source(
    mutation_name: &str,
    sql_source: Option<&str>,
    operation: &str,
    return_type: &str,
    crud: Option<&CrudNamingConfig>,
) -> Result<String> {
    if let Some(src) = sql_source {
        return Ok(src.to_string());
    }
    if let Some(cfg) = crud {
        let entity = pascal_to_snake(return_type);
        if let Some(resolved) = cfg.resolve(operation, &entity) {
            return Ok(resolved);
        }
    }
    anyhow::bail!(
        "Mutation '{mutation_name}' has no `sql_source` and no `[crud]` naming config \
         could resolve it (operation = {operation:?}, return_type = {return_type:?}). \
         Either add `sql_source` to the mutation or configure `[crud]` in fraiseql.toml."
    )
}

/// Lower `[[analytics.queries]]` into ordinary compiled queries (#624).
///
/// Each entry becomes a list-returning, view-backed `QueryDefinition`: the
/// operator-authored `sql_source` goes through the same compile-time SQL
/// identifier validation as every other query, and the SELECT list is the
/// declared `return_type`'s fields — so no client-supplied identifier can
/// reach `FROM` or the SELECT list (the P01 constraint, satisfied
/// structurally rather than by a new validator).
///
/// Fails loud on an unknown `return_type`, a name that collides with an
/// existing query, or a name ending in `_aggregate` / `_window` — the
/// executor's classifier dispatches those suffixes before query resolution,
/// so such a query would compile and then be unreachable.
fn apply_analytics_queries(
    analytics: &crate::config::toml_schema::AnalyticsConfig,
    queries_array: &mut Vec<Value>,
    types_array: &[Value],
) -> Result<()> {
    for query in &analytics.queries {
        if queries_array
            .iter()
            .any(|q| q.get("name").and_then(Value::as_str) == Some(query.name.as_str()))
        {
            anyhow::bail!(
                "[[analytics.queries]] name '{}' collides with an existing query; analytics \
                 queries share the query namespace.",
                query.name
            );
        }
        if query.name.ends_with("_aggregate") || query.name.ends_with("_window") {
            anyhow::bail!(
                "[[analytics.queries]] name '{}' ends in a reserved suffix: the executor \
                 dispatches `_aggregate` / `_window` root fields to the fact-table planners \
                 before query resolution, so this query would be unreachable. Rename it.",
                query.name
            );
        }
        let type_exists = types_array
            .iter()
            .any(|t| t.get("name").and_then(Value::as_str) == Some(query.return_type.as_str()));
        if !type_exists {
            let declared: Vec<&str> = types_array
                .iter()
                .filter_map(|t| t.get("name").and_then(Value::as_str))
                .collect();
            anyhow::bail!(
                "[[analytics.queries]] '{}' declares return_type '{}', which is not a \
                 declared type. Declared types: {}",
                query.name,
                query.return_type,
                declared.join(", ")
            );
        }
        queries_array.push(json!({
            "name": query.name,
            "return_type": query.return_type,
            "returns_list": true,
            "sql_source": query.sql_source,
            "description": query.description,
        }));
    }
    Ok(())
}

/// Lower `[[caching.rules]]` onto the compiled fields the runtime's result
/// cache consumes (#623): the named query's `cache_ttl_seconds` (per-view TTL
/// map, opt-in) and each trigger mutation's `invalidates_views`
/// (mutation-driven invalidation).
///
/// Fails loud on an unknown query, an unknown trigger mutation, a query with
/// no `sql_source`, or a TTL already authored on the query — a cache rule
/// that silently matches nothing, or silently loses to another authoring
/// source, is the #612 config-honesty bug this section was rejected over.
fn apply_caching_rules(
    caching: &crate::config::toml_schema::CachingConfig,
    queries_array: &mut [Value],
    mutations_array: &mut [Value],
) -> Result<()> {
    fn named<'a>(items: &'a mut [Value], name: &str) -> Option<&'a mut Value> {
        items.iter_mut().find(|i| i.get("name").and_then(Value::as_str) == Some(name))
    }
    fn names(items: &[Value]) -> String {
        items
            .iter()
            .filter_map(|i| i.get("name").and_then(Value::as_str))
            .collect::<Vec<_>>()
            .join(", ")
    }

    for rule in &caching.rules {
        let Some(query) = named(queries_array, &rule.query) else {
            anyhow::bail!(
                "[[caching.rules]] names query '{}', which does not exist. Declared \
                 queries: {}",
                rule.query,
                names(queries_array)
            );
        };
        if query.get("cache_ttl_seconds").is_some_and(|v| !v.is_null()) {
            anyhow::bail!(
                "[[caching.rules]] sets ttl_seconds for query '{}', but the query already \
                 declares cache_ttl_seconds (SDK/JSON-authored, or an earlier rule). Two \
                 authoring sources for one TTL must not silently last-write-win — remove \
                 one of them.",
                rule.query
            );
        }
        let Some(view) = query.get("sql_source").and_then(Value::as_str).map(str::to_owned) else {
            anyhow::bail!(
                "[[caching.rules]] targets query '{}', which has no sql_source; only \
                 view-backed queries are cacheable.",
                rule.query
            );
        };
        query["cache_ttl_seconds"] = json!(rule.ttl_seconds);

        for trigger in &rule.invalidation_triggers {
            let Some(mutation) = named(mutations_array, trigger) else {
                anyhow::bail!(
                    "[[caching.rules]] for query '{}' names invalidation trigger '{}', \
                     which is not a declared mutation. Declared mutations: {}",
                    rule.query,
                    trigger,
                    names(mutations_array)
                );
            };
            let views = mutation
                .as_object_mut()
                .expect("mutation entries are objects by construction")
                .entry("invalidates_views")
                .or_insert_with(|| json!([]));
            let list = views.as_array_mut().ok_or_else(|| {
                anyhow::anyhow!(
                    "mutation '{trigger}' has a non-array invalidates_views; cannot append"
                )
            })?;
            if !list.iter().any(|v| v.as_str() == Some(view.as_str())) {
                list.push(json!(view));
            }
        }
    }
    Ok(())
}

/// Serialize TOML-declared arguments through [`IntermediateArgument`].
///
/// The round trip through the typed struct is the point: it is what makes the emitted wire
/// keys (`type`, `nullable`) the ones the consumer reads, rather than a second spelling
/// maintained by hand in a `json!` literal (`#756`).
fn lower_toml_args(args: &[crate::config::toml_schema::ArgumentDefinition]) -> Result<Vec<Value>> {
    args.iter()
        .map(|arg| {
            serde_json::to_value(IntermediateArgument::from(arg))
                .with_context(|| format!("Failed to serialize declared argument {:?}", arg.name))
        })
        .collect()
}

/// Schema merger combining language types and TOML config
pub struct SchemaMerger;

impl SchemaMerger {
    /// Merge types.json file with TOML configuration
    ///
    /// # Arguments
    /// * `types_path` - Path to types.json (from language implementation)
    /// * `toml_path` - Path to fraiseql.toml (configuration)
    ///
    /// # Returns
    /// Combined `IntermediateSchema`.
    ///
    /// # Errors
    ///
    /// Returns an error if either file cannot be read or parsed, or if the
    /// merged result cannot be deserialized into an `IntermediateSchema`.
    pub fn merge_files(types_path: &str, toml_path: &str) -> Result<IntermediateSchema> {
        // Load types.json
        let types_json = fs::read_to_string(types_path)
            .context(format!("Failed to read types.json from {types_path}"))?;
        let types_value: Value =
            serde_json::from_str(&types_json).context("Failed to parse types.json")?;

        // Load TOML
        let toml_schema = TomlSchema::from_file(toml_path)
            .context(format!("Failed to load TOML from {toml_path}"))?;

        // Note: TOML validation is skipped here because queries may reference types
        // from types.json (not yet loaded). Validation happens in the compiler after merge.

        // Merge
        Self::merge_values(&types_value, &toml_schema)
    }

    /// Merge TOML-only (no types.json)
    ///
    /// # Arguments
    /// * `toml_path` - Path to fraiseql.toml with inline type definitions
    ///
    /// # Returns
    /// `IntermediateSchema` from TOML definitions.
    ///
    /// # Errors
    ///
    /// Returns an error if the TOML file cannot be loaded, if validation fails,
    /// or if the merged result cannot be deserialized into an `IntermediateSchema`.
    pub fn merge_toml_only(toml_path: &str) -> Result<IntermediateSchema> {
        let toml_schema = TomlSchema::from_file(toml_path)
            .context(format!("Failed to load TOML from {toml_path}"))?;

        toml_schema.validate()?;

        // Convert TOML to intermediate schema
        let types_value = toml_schema.to_intermediate_schema();
        Self::merge_values(&types_value, &toml_schema)
    }

    /// Merge from directory with auto-discovery
    ///
    /// # Arguments
    /// * `toml_path` - Path to fraiseql.toml (configuration)
    /// * `schema_dir` - Path to directory containing schema files
    ///
    /// # Returns
    /// `IntermediateSchema` from loaded files + TOML definitions.
    ///
    /// # Errors
    ///
    /// Returns an error if either file cannot be loaded or validated, if the
    /// directory cannot be read, or if the merged result cannot be deserialized.
    pub fn merge_from_directory(toml_path: &str, schema_dir: &str) -> Result<IntermediateSchema> {
        let toml_schema = TomlSchema::from_file(toml_path)
            .context(format!("Failed to load TOML from {toml_path}"))?;

        toml_schema.validate()?;

        // Load all files from directory
        let types_value = crate::schema::MultiFileLoader::load_from_directory(schema_dir)
            .context(format!("Failed to load schema from directory {schema_dir}"))?;

        // Merge with TOML definitions
        Self::merge_values(&types_value, &toml_schema)
    }

    /// Load every section from a set of files, returning `None` when the list is empty.
    fn load_all_sections(files: &[String]) -> Result<Option<serde_json::Value>> {
        if files.is_empty() {
            return Ok(None);
        }
        let paths: Vec<std::path::PathBuf> = files.iter().map(std::path::PathBuf::from).collect();
        let loaded = crate::schema::MultiFileLoader::load_from_paths(&paths)
            .context("Failed to load explicit schema files")?;
        Ok(Some(loaded))
    }

    /// Parse a JSON file and absorb **every** authorable section into the accumulator.
    ///
    /// This used to read exactly `types`, `queries` and `mutations`, with the comment
    /// "Missing keys are silently skipped" — which is how a domain that declared enums
    /// compiled successfully without them (`#755`). The section list now lives in one
    /// place, so this site cannot fall behind the others.
    fn extend_from_json_file(path: &std::path::Path, accumulator: &mut Value) -> Result<()> {
        let content = fs::read_to_string(path)
            .with_context(|| format!("Failed to read {}", path.display()))?;
        let value: Value = serde_json::from_str(&content)
            .with_context(|| format!("Failed to parse {}", path.display()))?;
        super::seam::absorb_sections(accumulator, &value, &path.display().to_string())
    }

    /// Apply TOML metadata (`sql_source`, `description`) to a type JSON object in place.
    fn enrich_type_from_toml(
        enriched_type: &mut Value,
        toml_type: &crate::config::toml_schema::TypeDefinition,
    ) {
        // The overlay half of the shared emitter (#1266): every key TOML contributes to
        // a type, minus identity and `fields`, which the SDK's `schema.json` owns here.
        // Written as a merge rather than a replacement for that reason — and reading the
        // key list from one place is what stops a new TOML type key from reaching the
        // compiler on the TOML-only path and vanishing on the `--types` one.
        for (key, value) in toml_type.intermediate_overlay() {
            enriched_type[key] = value;
        }
    }

    /// Merge explicit file lists
    ///
    /// # Arguments
    /// * `toml_path` - Path to fraiseql.toml (configuration)
    /// * `type_files` - Vector of type file paths
    /// * `query_files` - Vector of query file paths
    /// * `mutation_files` - Vector of mutation file paths
    ///
    /// # Returns
    /// `IntermediateSchema` from loaded files + TOML definitions
    ///
    /// # Errors
    ///
    /// Returns an error if the TOML file cannot be loaded or validated, or if any
    /// of the type/query/mutation files fail to load or parse.
    pub fn merge_explicit_files(
        toml_path: &str,
        type_files: &[String],
        query_files: &[String],
        mutation_files: &[String],
    ) -> Result<IntermediateSchema> {
        let toml_schema = TomlSchema::from_file(toml_path)
            .context(format!("Failed to load TOML from {toml_path}"))?;

        toml_schema.validate()?;

        let mut types_value = super::seam::empty_accumulator();

        // Absorb each file list wholesale rather than lifting one key out of it: a
        // `--type-files` entry that also declares enums used to have those enums read and
        // then discarded, because `load_section` returned only the caller's named key.
        for files in [type_files, query_files, mutation_files] {
            if let Some(loaded) = Self::load_all_sections(files)? {
                super::seam::absorb_sections(&mut types_value, &loaded, "explicit schema files")?;
            }
        }

        Self::merge_values(&types_value, &toml_schema)
    }

    /// Merge from domains (domain-based organization)
    ///
    /// # Arguments
    /// * `toml_path` - Path to fraiseql.toml with domain_discovery enabled
    ///
    /// # Returns
    /// `IntermediateSchema` from all domains (types.json, queries.json, mutations.json).
    ///
    /// # Errors
    ///
    /// Returns an error if the TOML cannot be loaded or validated, if domain
    /// discovery fails, if any domain file cannot be parsed, or if the merged
    /// result cannot be deserialized.
    pub fn merge_from_domains(toml_path: &str) -> Result<IntermediateSchema> {
        let toml_schema = TomlSchema::from_file(toml_path)
            .context(format!("Failed to load TOML from {toml_path}"))?;

        toml_schema.validate()?;

        // Resolve domains from configuration
        let domains = toml_schema
            .domain_discovery
            .resolve_domains()
            .context("Failed to discover domains")?;

        if domains.is_empty() {
            // No domains found, return empty schema merged with TOML definitions
            return Self::merge_values(&super::seam::empty_accumulator(), &toml_schema);
        }

        let mut types_value = super::seam::empty_accumulator();

        for domain in domains {
            for filename in ["types.json", "queries.json", "mutations.json"] {
                let path = domain.path.join(filename);
                if path.exists() {
                    Self::extend_from_json_file(&path, &mut types_value)?;
                }
            }
        }

        // Merge with TOML definitions
        Self::merge_values(&types_value, &toml_schema)
    }

    /// Merge with TOML includes (glob patterns for schema files)
    ///
    /// # Arguments
    /// * `toml_path` - Path to fraiseql.toml with schema.includes section
    ///
    /// # Returns
    /// `IntermediateSchema` from loaded files + TOML definitions.
    ///
    /// # Errors
    ///
    /// Returns an error if the TOML cannot be loaded or validated, if any glob
    /// pattern is invalid, if a matched file cannot be parsed, or if the merged
    /// result cannot be deserialized.
    pub fn merge_with_includes(toml_path: &str) -> Result<IntermediateSchema> {
        let toml_schema = TomlSchema::from_file(toml_path)
            .context(format!("Failed to load TOML from {toml_path}"))?;

        toml_schema.validate()?;

        // If includes are specified, load and merge files.
        //
        // Every resolved glob group is absorbed whole. The previous shape lifted a single
        // named key out of each group (`loaded.get("queries")`, `loaded.get("mutations")`),
        // so an included file that declared anything else contributed nothing (`#755`).
        let mut types_value = super::seam::empty_accumulator();
        if !toml_schema.includes.is_empty() {
            let resolved = toml_schema
                .includes
                .resolve_globs()
                .context("Failed to resolve glob patterns in schema.includes")?;

            for group in [&resolved.types, &resolved.queries, &resolved.mutations] {
                if group.is_empty() {
                    continue;
                }
                let loaded = crate::schema::MultiFileLoader::load_from_paths(group)
                    .context("Failed to load included schema files")?;
                super::seam::absorb_sections(&mut types_value, &loaded, "schema.includes")?;
            }
        }

        // Merge with TOML definitions
        Self::merge_values(&types_value, &toml_schema)
    }

    /// Merge JSON types with TOML schema
    #[allow(clippy::cognitive_complexity)] // Reason: deep merge of two schema formats with many field-level transformations
    fn merge_values(types_value: &Value, toml_schema: &TomlSchema) -> Result<IntermediateSchema> {
        // #1017: every self-contained TOML check runs on EVERY compile path, here at
        // the funnel all six `merge_*` entry points share.
        //
        // `merge_files` (the `--types` workflow) cannot call the whole of
        // `TomlSchema::validate()`, because a query in the TOML may legitimately name a
        // type that only `types.json` defines. That exemption justifies skipping the
        // type-reference checks and nothing else — but for a long time it skipped all of
        // them, so an invalid `[server]` port, a `pool_min` above `pool_max`, an
        // incomplete `[auth]` PKCE group and an unparseable proxy CIDR were refused by
        // five workflows and compiled by the sixth. #612's unconsumed-config gate, #892's
        // `[tenancy]` check and #897's role check were each rescued here one at a time;
        // calling the self-contained half wholesale is what stops the next one needing
        // the same rescue.
        //
        // The other five entry points call `TomlSchema::validate()`, which runs this half
        // too, so they check it twice. That redundancy is the point and must not be
        // "cleaned up" by dropping this call: it is what makes the funnel — not the
        // entry point — the thing that guarantees the check ran.
        toml_schema.validate_self_contained()?;

        // Typo guard: [queries.defaults] is a common mistake for [query_defaults].
        if toml_schema.queries.contains_key("defaults") {
            anyhow::bail!(
                "Found a query definition named 'defaults' under [queries.defaults]. \
                 Did you mean [query_defaults] to set global auto-param defaults?\n\
                 If you intended a query called 'defaults', rename it to avoid confusion."
            );
        }

        // Start with arrays for types, queries, mutations (not objects!)
        // This matches IntermediateSchema structure which uses Vec<T>
        let mut types_array: Vec<Value> = Vec::new();
        let mut queries_array: Vec<Value> = Vec::new();
        let mut mutations_array: Vec<Value> = Vec::new();

        // Process types from types.json (comes as array from language SDKs)
        if let Some(types_obj) = types_value.get("types") {
            match types_obj {
                // Handle array format (from language SDKs)
                Value::Array(types_list) => {
                    for type_item in types_list {
                        if let Some(type_name) = type_item.get("name").and_then(|v| v.as_str()) {
                            let mut enriched_type = type_item.clone();
                            if let Some(toml_type) = toml_schema.types.get(type_name) {
                                Self::enrich_type_from_toml(&mut enriched_type, toml_type);
                            }
                            types_array.push(enriched_type);
                        }
                    }
                },
                // Handle object format (from TOML-only, for backward compatibility)
                Value::Object(types_map) => {
                    for (type_name, type_value) in types_map {
                        let mut enriched_type = type_value.clone();
                        enriched_type["name"] = json!(type_name);

                        // Convert fields from object to array format if needed
                        if let Some(Value::Object(fields_map)) = enriched_type.get("fields") {
                            let fields_array: Vec<Value> = fields_map
                                .iter()
                                .map(|(field_name, field_value)| {
                                    let mut field = field_value.clone();
                                    field["name"] = json!(field_name);
                                    field
                                })
                                .collect();
                            enriched_type["fields"] = json!(fields_array);
                        }

                        if let Some(toml_type) = toml_schema.types.get(type_name) {
                            Self::enrich_type_from_toml(&mut enriched_type, toml_type);
                        }

                        types_array.push(enriched_type);
                    }
                },
                _ => {},
            }
        }

        // Add types from TOML that aren't already in types_array
        let existing_type_names: std::collections::HashSet<_> = types_array
            .iter()
            .filter_map(|t| t.get("name").and_then(|v| v.as_str()).map(str::to_string))
            .collect();

        for (type_name, toml_type) in &toml_schema.types {
            if !existing_type_names.contains(type_name) {
                // One emitter, shared with `TomlSchema::to_intermediate_schema` (#959,
                // widened from fields to the whole type by #1266): the hand-built copies
                // had drifted, and the symptom of the drift is an authored key that
                // silently does nothing on one of the TOML paths.
                types_array.push(toml_type.to_intermediate_json(type_name));
            }
        }

        if let Some(Value::Array(queries_list)) = types_value.get("queries") {
            queries_array.clone_from(queries_list);
        }

        // Add queries from TOML
        for (query_name, toml_query) in &toml_schema.queries {
            queries_array.push(json!({
                "name": query_name,
                "return_type": toml_query.return_type,
                "returns_list": toml_query.return_array,
                "sql_source": toml_query.sql_source,
                "description": toml_query.description,
                "arguments": lower_toml_args(&toml_query.args)?,
            }));
        }

        if let Some(Value::Array(mutations_list)) = types_value.get("mutations") {
            mutations_array.clone_from(mutations_list);
        }

        // Add mutations from TOML
        for (mutation_name, toml_mutation) in &toml_schema.mutations {
            let sql_source = resolve_mutation_sql_source(
                mutation_name,
                toml_mutation.sql_source.as_deref(),
                &toml_mutation.operation,
                &toml_mutation.return_type,
                toml_schema.crud.as_ref(),
            )?;
            mutations_array.push(json!({
                "name": mutation_name,
                "return_type": toml_mutation.return_type,
                "sql_source": sql_source,
                "operation": toml_mutation.operation,
                "input_style": toml_mutation.input_style,
                "changelog_pre_image": toml_mutation.changelog_pre_image,
                "cascade": toml_mutation.cascade,
                "description": toml_mutation.description,
                "arguments": lower_toml_args(&toml_mutation.args)?,
            }));
        }

        // #624: lower [[analytics.queries]] into ordinary compiled queries —
        // before the caching rules, so a [[caching.rules]] entry can target an
        // analytics query.
        apply_analytics_queries(&toml_schema.analytics, &mut queries_array, &types_array)?;

        // #623: lower [[caching.rules]] onto the compiled fields the runtime's
        // result cache consumes. Runs after both arrays hold every authored
        // operation (JSON/SDK and TOML alike), so a rule can target either.
        apply_caching_rules(&toml_schema.caching, &mut queries_array, &mut mutations_array)?;

        // Build the merged schema by **carrying the authored document forward** and
        // overwriting only the three sections this function actually transforms.
        //
        // This used to be `json!({version, types, queries, mutations})` — a fresh object
        // built from scratch, which silently discarded every other section the SDK had
        // authored: enums, input types, interfaces, unions, subscriptions, observers,
        // custom scalars, sources, session variables and federation (`#755`). Eight
        // categories, on all five TOML-workflow compile paths, with `✓ Schema compiled
        // successfully` printed.
        //
        // Pass-through inverts the default: a section the merger does not understand
        // survives to `IntermediateSchema`, which either binds it or — since it now denies
        // unknown fields — refuses the compile. Neither outcome is silent, and a section
        // added tomorrow needs no change here.
        let mut merged = types_value.clone();
        if !merged.is_object() {
            anyhow::bail!(
                "Expected a JSON object at the top level of the schema input, found {}",
                if merged.is_array() {
                    "an array"
                } else {
                    "a scalar"
                }
            );
        }
        merged["version"] = json!("2.0.0");
        merged["types"] = json!(types_array);
        merged["queries"] = json!(queries_array);
        merged["mutations"] = json!(mutations_array);

        // Warn when PKCE is enabled without state encryption (insecure configuration).
        if let Some(pkce) = &toml_schema.security.pkce {
            if pkce.enabled {
                let enc_enabled =
                    toml_schema.security.state_encryption.as_ref().is_some_and(|e| e.enabled);
                if !enc_enabled {
                    tracing::warn!(
                        "pkce.enabled = true but state_encryption.enabled = false. \
                         PKCE state will be stored unencrypted. \
                         Set [security.state_encryption] enabled = true for production."
                    );
                }
            }
        }

        // Add security configuration if available in TOML.
        //
        // Constructed as the typed `fraiseql_core::schema::SecurityConfig` and
        // serialized (#977): the compiled seam owns every section's shape and is
        // `deny_unknown_fields`, so a key this block emitted under the wrong
        // name would fail to deserialize instead of landing in a catch-all.
        // Building the struct — rather than writing key names by hand — makes
        // that drift a compile error here, before it can reach a file.
        // `tenancy_gate_seam_test` additionally asks the consumer's questions of
        // a compiled file rather than checking key presence.
        let sec = &toml_schema.security;
        merged["security"] = serde_json::to_value(fraiseql_core::schema::SecurityConfig {
            // #897: lowered from `[[security.role_definitions]]` / `default_role`, through
            // the same `to_runtime` the project-config producer uses. Hard-coded empty
            // until then, which made field-level RBAC undeclarable on this workflow: a
            // field marked `requires_scope` was denied to everyone, because no role could
            // be defined to grant the scope.
            role_definitions:       sec
                .role_definitions
                .iter()
                .map(crate::config::security::RoleDefinitionConfig::to_runtime)
                .collect(),
            default_role:           sec.default_role.clone(),
            multi_tenant:           sec.multi_tenant,
            rls:                    sec.rls.clone(),
            // #892: lowered from `[tenancy]`, through the same `to_runtime` the project-
            // config path uses. Hard-coded to the default until then, which made
            // `tenancy.mode` — and so schema-per-tenant provisioning, row-mode
            // `@tenant_id` validation and `is_multi_tenant()` — unreachable from this
            // workflow and from every `[domain_discovery]` project.
            tenancy:                toml_schema.tenancy.to_runtime(),
            cost_budget:            sec.cost_budget.clone(),
            // #983: not emitted — no consumer reads it, and every Workflow-A schema
            // used to carry `"authenticated"` here by default, which is precisely the
            // kind of declaration an operator reads as an enforced boundary.
            default_policy:         None,
            rules:                  sec.rules.clone(),
            policies:               sec.policies.clone(),
            field_auth:             sec.field_auth.clone(),
            enterprise:             Some(sec.enterprise.clone()),
            error_sanitization:     sec.error_sanitization.clone(),
            rate_limiting:          sec.rate_limiting.clone(),
            state_encryption:       sec.state_encryption.clone(),
            pkce:                   sec.pkce.clone(),
            api_keys:               sec.api_keys.clone(),
            token_revocation:       sec.token_revocation.clone(),
            trusted_documents:      sec.trusted_documents.clone(),
            persisted_queries_only: sec.persisted_queries_only,
            service_accounts:       None,
        })
        .context("Failed to serialize [security] into the compiled schema")?;

        // Embed observers configuration if enabled or if any backend URL is set
        if toml_schema.observers.is_configured() {
            if toml_schema.observers.backend == fraiseql_core::schema::ObserversBackend::Nats
                && toml_schema.observers.nats_url.is_none()
            {
                tracing::warn!(
                    "observers.backend is \"nats\" but observers.nats_url is not set; \
                     the runtime will require FRAISEQL_NATS_URL to be configured"
                );
            }
            // No `handlers` key (#631): compiled handler declarations are not a
            // runtime concept — TOML validation has already rejected a non-empty
            // `[[observers.handlers]]`, and the compiled `ObserversConfig` is
            // `deny_unknown_fields` so the key cannot be represented.
            merged["observers_config"] = serde_json::to_value(toml_schema.observers.to_compiled())
                .context("Failed to serialize observers config")?;
        }

        // Embed the `[functions]` settings when the project configures any (#1325).
        // A table left at its defaults produces no section: an empty one would read
        // as a deliberate choice, and the compiler's own `functions/` convention is
        // the honest answer to "the author said nothing".
        if toml_schema.functions.is_configured() {
            merged["functions_config"] = json!({
                "module_dir": toml_schema.functions.module_dir,
                "dlq_store": toml_schema.functions.dlq_store,
            });
        }

        // Embed federation configuration if enabled. Lower the TOML config into the
        // compiled (`fraiseql_core`) shape explicitly so the merged JSON matches what
        // the converter/runtime deserialize — a raw passthrough silently dropped
        // `service_name`/`version` and the `per_database` → `per_entity` overrides.
        if toml_schema.federation.enabled {
            merged["federation_config"] =
                serde_json::to_value(toml_schema.federation.to_compiled())
                    .context("Failed to serialize federation config")?;
        }

        // Embed the `[auth]` OAuth-client groups. The PKCE group (#621) is
        // all-four-or-none (enforced by `OidcClientConfig::validate` at load
        // time), so if `client_id` is present the whole group is; it lowers into
        // the compiled `auth.pkce` object, which carries the client identity and
        // the provider `discovery_url` only — the runtime resolves the
        // authorization/token endpoints at boot, and the secret is read from
        // `client_secret_env`, never embedded. The social group (#368,
        // `[auth.social.*]`) is already authored in the compiled type and is
        // embedded verbatim under `auth.social`.
        if let Some(auth) = &toml_schema.auth {
            let mut auth_obj = serde_json::Map::new();
            if let (Some(discovery_url), Some(client_id), Some(client_secret_env), Some(redirect)) = (
                auth.discovery_url.as_ref(),
                auth.client_id.as_ref(),
                auth.client_secret_env.as_ref(),
                auth.server_redirect_uri.as_ref(),
            ) {
                auth_obj.insert(
                    "pkce".to_string(),
                    json!({
                        "discovery_url": discovery_url,
                        "client_id": client_id,
                        "client_secret_env": client_secret_env,
                        "server_redirect_uri": redirect,
                    }),
                );
            }
            if let Some(social) = &auth.social {
                auth_obj.insert(
                    "social".to_string(),
                    serde_json::to_value(social).context("Failed to serialize [auth.social]")?,
                );
            }
            if let Some(local) = &auth.local {
                auth_obj.insert(
                    "local".to_string(),
                    serde_json::to_value(local).context("Failed to serialize [auth.local]")?,
                );
            }
            if let Some(session) = &auth.session {
                auth_obj.insert(
                    "session".to_string(),
                    serde_json::to_value(session).context("Failed to serialize [auth.session]")?,
                );
            }
            if let Some(database) = &auth.database {
                auth_obj.insert(
                    "database".to_string(),
                    serde_json::to_value(database)
                        .context("Failed to serialize [auth.database]")?,
                );
            }
            if !auth_obj.is_empty() {
                merged["auth"] = serde_json::Value::Object(auth_obj);
            }
        }

        // Embed subscriptions configuration (hooks, limits)
        let subs_json = serde_json::to_value(&toml_schema.subscriptions)
            .context("Failed to serialize subscriptions config")?;
        if subs_json != serde_json::json!({}) {
            merged["subscriptions_config"] = subs_json;
        }

        // Embed validation config (depth/complexity limits)
        let val_json = serde_json::to_value(&toml_schema.validation)
            .context("Failed to serialize validation config")?;
        if val_json != serde_json::json!({}) {
            merged["validation_config"] = val_json;
        }

        // Embed debug config when enabled
        if toml_schema.debug.enabled {
            let debug_json = serde_json::to_value(&toml_schema.debug)
                .context("Failed to serialize debug config")?;
            merged["debug_config"] = debug_json;
        }

        // Embed MCP config when enabled
        if toml_schema.mcp.enabled {
            merged["mcp_config"] =
                serde_json::to_value(&toml_schema.mcp).context("Failed to serialize MCP config")?;
        }

        // Embed REST config when enabled (with path validation)
        if toml_schema.rest.enabled {
            let path = &toml_schema.rest.path;
            if !path.starts_with('/') {
                anyhow::bail!("REST config: `path` must start with '/' (got {path:?})");
            }

            let rest_config: fraiseql_core::schema::RestConfig = toml_schema.rest.clone().into();

            merged["rest_config"] =
                serde_json::to_value(&rest_config).context("Failed to serialize REST config")?;
        }

        // Embed gRPC config when enabled (#780).
        //
        // `descriptor_path` is validated here rather than at boot: `build_grpc_service` reads
        // the FileDescriptorSet from that path, so an empty one guarantees a server that
        // cannot mount the transport it was told to enable. Failing at compile time is the
        // difference between a message naming the TOML key and a runtime read error.
        if toml_schema.grpc.enabled {
            if toml_schema.grpc.descriptor_path.trim().is_empty() {
                anyhow::bail!(
                    "[grpc] enabled = true requires `descriptor_path`, the path to the \
                     FileDescriptorSet binary (.binpb) the transport serves. Generate one with \
                     `protoc --descriptor_set_out`, or set `enabled = false`."
                );
            }
            if toml_schema.grpc.stream_batch_size == 0 {
                anyhow::bail!(
                    "[grpc] stream_batch_size must be greater than 0 (got 0) — a zero batch \
                     size would make every server-streaming response empty."
                );
            }
            merged["grpc_config"] = serde_json::to_value(&toml_schema.grpc)
                .context("Failed to serialize gRPC config")?;
        }

        // Embed naming convention
        merged["naming_convention"] = serde_json::to_value(toml_schema.naming_convention)
            .context("Failed to serialize naming_convention")?;

        // Embed changelog GraphQL-exposure config (gating + injection happen in the converter)
        if let Some(ref changelog) = toml_schema.changelog {
            merged["changelog_config"] =
                serde_json::to_value(changelog).context("Failed to serialize changelog config")?;
        }

        // Embed hierarchy definitions for ID-based ltree operators
        if let Some(ref hierarchies) = toml_schema.hierarchies {
            merged["hierarchies_config"] = serde_json::to_value(hierarchies)
                .context("Failed to serialize hierarchies config")?;
        }

        // Embed per-request session variables. Serialized from the same type the
        // runtime deserializes, so the mapping an RLS policy depends on cannot be
        // lost to a key rename here (#628).
        if toml_schema.session_variables != fraiseql_core::schema::SessionVariablesConfig::default()
        {
            merged["session_variables"] = serde_json::to_value(&toml_schema.session_variables)
                .context("Failed to serialize session_variables")?;
        }

        // `[locale]` (#1512): serialized from the type the runtime deserializes.
        if let Some(locale) = &toml_schema.locale {
            merged["locale"] =
                serde_json::to_value(locale).context("Failed to serialize locale")?;
        }

        // `[inject_defaults]` (#1384): the TOML schema's section, reconciled with a block the
        // SDK may have emitted into types.json from the same config.
        let document_defaults = merged
            .get("inject_defaults")
            .cloned()
            .map(serde_json::from_value::<super::intermediate::IntermediateInjectDefaults>)
            .transpose()
            .context("Invalid inject_defaults in the merged schema document")?;
        if let Some(defaults) = crate::config::inject_defaults::InjectDefaultsToml::reconcile(
            toml_schema.inject_defaults.as_ref(),
            document_defaults,
        )? {
            merged["inject_defaults"] =
                serde_json::to_value(defaults).context("Failed to serialize inject_defaults")?;
        }

        // Refuse a security control declared under a key that does not bind (#806/#807).
        //
        // This is the TOML / multi-file workflow's *only* deserialization point — all six
        // `merge_*` entry points funnel through `merge_values` — and it is a genuinely
        // separate seam from the JSON workflow's guard in `commands::compile`. Guarding
        // only the JSON path would have left every `--schema-dir` and `types.json` user
        // with the original silent drop, which is the shape of defect this guard exists
        // to close: a check that exists and has a call site routing around it.
        super::intermediate::reject_drifted_keys(&merged).map_err(|e| anyhow::anyhow!("{e}"))?;

        // Convert to IntermediateSchema
        let mut schema = serde_json::from_value::<IntermediateSchema>(merged)
            .context("Failed to convert merged schema to IntermediateSchema")?;

        // Inject TOML [query_defaults] into the schema so the converter can apply
        // them as project-wide fallbacks for list-query auto-params.
        schema.query_defaults = Some(IntermediateQueryDefaults {
            where_clause:     toml_schema.query_defaults.where_clause,
            order_by:         toml_schema.query_defaults.order_by,
            limit:            toml_schema.query_defaults.limit,
            offset:           toml_schema.query_defaults.offset,
            pagination_order: toml_schema.query_defaults.pagination_order,
        });

        Ok(schema)
    }
}