fix(config): tolerate JSONC when reading agent config files

[getappz]

Summary

json_at()/merge_json()/merge_opencode_mcp() (src/components.rs) and wire_opencode() (src/init.rs) all read an existing agent config file with plain serde_json::from_str before merging in agentflare's own entries.

opencode.jsonc (and the JSONC dialect several editors use for settings.json/mcp.json) commonly contains ////* */ comments and trailing commas — both invalid strict JSON. A real user's opencode.jsonc with comments silently fails to parse, and every one of these call sites was treating that parse failure as "no config yet" — so agentflare init/component-apply would overwrite the file with just agentflare's own entry, silently dropping the user's existing mcp servers, model settings, and instructions.

Fix

Adds src/jsonc.rs::parse_jsonc (strip ////* */ comments, strip trailing commas before }/], then serde_json::from_str; string contents preserved verbatim, multi-byte UTF-8 never split — ported and adapted from lean-ctx's core/jsonc.rs) and wires it into all four read sites. A jsonc-tolerant parser is a strict superset of JSON, so this is safe for the non-jsonc config files that also route through json_at/merge_json (cursor/windsurf/vscode-copilot/cline mcp.json).

Regression tests added for both the components.rs merge path and init.rs's wire_opencode path, each constructing a real jsonc file (comments + trailing comma + an existing entry) and asserting the existing entry survives the write.

Testing

• cargo test --workspace — 392 passed, 0 failed
• cargo clippy --workspace --all-targets -- -D warnings -A unsafe_code -A clippy::pedantic — clean
• cargo fmt --check — clean

Summary by CodeRabbit

• Bug Fixes
  • Improved configuration handling for JSONC files, including comments and trailing commas.
  • Preserved existing MCP server entries when updating OpenCode configuration.
  • Prevented configuration data from being lost when applying components or wiring instructions.

[coderabbitai]

📝 Walkthrough

Walkthrough

This change adds JSONC parsing with support for comments and trailing commas, then uses it when merging component configurations and wiring OpenCode instructions while preserving existing configuration entries.

Changes

JSONC configuration support

Layer / File(s)	Summary
JSONC parser and coverage src/main.rs, src/jsonc.rs	Adds parse_jsonc, comment and trailing-comma handling, and comprehensive parser tests.
Component configuration merging src/components.rs	Component and OpenCode MCP merges now parse JSONC input and verify existing MCP entries are preserved.
OpenCode initialization wiring src/init.rs	OpenCode initialization parses opencode.jsonc and tests preservation of MCP entries while wiring exa.md.

Estimated code review effort: 3 (Moderate) | ~30 minutes

Possibly related PRs

• getappz/agentflare#157: Also modifies OpenCode MCP merging and registration semantics.
• getappz/agentflare#171: Also changes MCP component wiring and merge_json behavior.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title clearly summarizes the main change: making config reads tolerate JSONC files.
Description check	✅ Passed	The PR description covers the summary, fix, and testing details, though it doesn't follow the template headings exactly.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch fix/jsonc-parser-for-agent-configs

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[coderabbitai]

🧹 Nitpick comments (2)

src/jsonc.rs (1)

17-39: 📐 Maintainability & Code Quality | 🔵 Trivial | ⚡ Quick win

Duplicate string-skipping logic in strip_json_comments and strip_trailing_commas.

The byte-level loop that skips over a "..." string (including escape handling) is copy-pasted verbatim in both functions. Any future fix to string/escape handling (e.g. a corner case) would need to be applied twice.

♻️ Proposed refactor: extract shared helper

/// Advances past a `"..."` string starting at `bytes[i] == b'"'`, honoring
/// backslash escapes. Returns the index just past the closing quote (or
/// `bytes.len()` if unterminated).
fn skip_string(bytes: &[u8], mut i: usize) -> usize {
    let len = bytes.len();
    i += 1;
    while i < len {
        let c = bytes[i];
        i += 1;
        if c == b'\\' && i < len {
            i += 1;
        } else if c == b'"' {
            break;
        }
    }
    i
}

Then in both strip_json_comments and strip_trailing_commas:

         if b == b'"' {
-            i += 1;
-            while i < len {
-                let c = bytes[i];
-                i += 1;
-                if c == b'\\' && i < len {
-                    i += 1;
-                } else if c == b'"' {
-                    break;
-                }
-            }
+            i = skip_string(bytes, i);
             continue;
         }

Also applies to: 78-100

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@src/jsonc.rs` around lines 17 - 39, Extract the duplicated quoted-string
scanning logic into a shared skip_string helper that accepts the byte slice and
starting quote index, preserves escape handling, and returns the index after the
closing quote or the input length if unterminated. Replace the inline loops in
both strip_json_comments and strip_trailing_commas with this helper.

src/components.rs (1)

50-55: 📐 Maintainability & Code Quality | 🔵 Trivial | ⚡ Quick win

Extract a shared read_jsonc(path, default) helper. The same read-file → parse_jsonc → fallback-on-failure boilerplate is duplicated across four call sites. A single helper centralizes the JSONC-read contract and avoids a future config-reading site forgetting to use parse_jsonc (the exact class of bug this PR fixes).

• src/components.rs#L50-L55: replace the json_at body with a call to the shared helper (default Value::Null).
• src/components.rs#L83-L104: replace the read+parse+fallback lines in merge_json with the shared helper (default json!({})).
• src/components.rs#L106-L151: replace the read+parse+fallback lines in merge_opencode_mcp with the shared helper (default json!({})).
• src/init.rs#L503-L575: replace the read+parse+fallback lines in wire_opencode with the shared helper (default json!({})).

♻️ Proposed helper

// src/jsonc.rs
pub fn read_jsonc(path: &std::path::Path, default: impl FnOnce() -> Value) -> Value {
    std::fs::read_to_string(path)
        .ok()
        .and_then(|s| parse_jsonc(&s).ok())
        .unwrap_or_else(default)
}

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@src/components.rs` around lines 50 - 55, Introduce a shared read_jsonc helper
in src/jsonc.rs that reads a path, parses it with parse_jsonc, and invokes a
lazy default on any failure. Update json_at in src/components.rs (lines 50-55)
to use it with Value::Null; update merge_json (lines 83-104) and
merge_opencode_mcp (lines 106-151) to use it with json!({}); and update
wire_opencode in src/init.rs (lines 503-575) with the same object default.

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Nitpick comments:
In `@src/components.rs`:
- Around line 50-55: Introduce a shared read_jsonc helper in src/jsonc.rs that
reads a path, parses it with parse_jsonc, and invokes a lazy default on any
failure. Update json_at in src/components.rs (lines 50-55) to use it with
Value::Null; update merge_json (lines 83-104) and merge_opencode_mcp (lines
106-151) to use it with json!({}); and update wire_opencode in src/init.rs
(lines 503-575) with the same object default.

In `@src/jsonc.rs`:
- Around line 17-39: Extract the duplicated quoted-string scanning logic into a
shared skip_string helper that accepts the byte slice and starting quote index,
preserves escape handling, and returns the index after the closing quote or the
input length if unterminated. Replace the inline loops in both
strip_json_comments and strip_trailing_commas with this helper.

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ℹ️ Review info

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Run ID: 036ce7f3-475c-4923-8d99-1c63b6989b52

📥 Commits

Reviewing files that changed from the base of the PR and between 82b2908 and 28abd01.

📒 Files selected for processing (4)

• src/components.rs
• src/init.rs
• src/jsonc.rs
• src/main.rs