fix(setup-wizard): stop replacing IDE settings that are JSONC by AloysJehwin · Pull Request #1677 · CodeGraphContext/CodeGraphContext

AloysJehwin · 2026-08-27T17:39:57Z

The wizard read the target settings file like this:

try:
    settings = json.load(f)
except json.JSONDecodeError:
    settings = {}

and then wrote settings back over the same file. VS Code and its forks write settings.json as JSONC, so a file with // comments or a trailing comma raises JSONDecodeError — the wizard read that as "no settings yet" and replaced the whole configuration with a lone mcpServers key. Two people on the issue lost their settings this way; one only recovered because Settings Sync was on.

Three changes:

Parse JSONC before giving up. _strip_jsonc removes // and /* */ comments and trailing commas, tracking string state so a // inside a URL or an escaped quote is left alone.
If it still will not parse, print why and return without writing. That fallback to {} was the actual data loss; an unreadable file should be left alone, not replaced.
Back up the file to .cgc-backup before writing, and say so when comments were present, since json.dump cannot preserve them. The backup keeps them.

Comment preservation on the rewritten file would need a JSONC-aware writer and a new dependency, so I kept it to the data loss and made the tradeoff visible instead of silent. Happy to go further if you would rather.

Tests: tests/unit/cli/test_setup_wizard_jsonc.py, 10 passing. They cover line and block comments, trailing commas, comment markers inside strings and URLs, a realistic commented settings.json keeping every key across a round trip, and that unparseable input raises rather than resolving to {}.

$ python -m pytest tests/unit/cli/test_setup_wizard_jsonc.py -q
..........                                                               [100%]
10 passed in 0.82s

Fixes #660

VS Code and its forks write settings.json as JSONC. json.load rejects comments and trailing commas, and the wizard treated that rejection as "no settings yet" before writing the file back, so a user's whole configuration was replaced by a lone mcpServers key. Parse JSONC before giving up, and if the file still cannot be parsed, leave it alone instead of overwriting it. Back up the file before writing either way, and say so when comments are present, since json.dump cannot preserve them. Fixes CodeGraphContext#660 Signed-off-by: Aloys Jehwin <[email protected]>

vercel · 2026-08-27T17:40:02Z

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Shashankss1205

Verified on a local trial-merge: the string-aware JSONC stripper handles comments inside strings and escapes correctly, the destructive except → settings = {} fallback is gone (an unreadable file is now left untouched with manual instructions), a backup is taken before every rewrite, and the dropped-comments note is honest about JSON's limits. All 10 new tests pass; full suite green. This closes a genuine data-loss hazard — VS Code settings.json is JSONC more often than not. Thanks @AloysJehwin!

* fix(viz): display source filenames for synthetic module nodes * fix(jobs): serialize last update time in job responses (#1679) * fix(cli): explain embedded database lock conflicts (#1684) * fix(setup-wizard): stop replacing IDE settings that are JSONC (#1677) VS Code and its forks write settings.json as JSONC. json.load rejects comments and trailing commas, and the wizard treated that rejection as "no settings yet" before writing the file back, so a user's whole configuration was replaced by a lone mcpServers key. Parse JSONC before giving up, and if the file still cannot be parsed, leave it alone instead of overwriting it. Back up the file before writing either way, and say so when comments are present, since json.dump cannot preserve them. Fixes #660 Signed-off-by: Aloys Jehwin <[email protected]> * feat(cgcignore): treat .gitignore as an ignore source (#1680) Anything git ignores is now ignored by the indexer, so a repository no longer needs a .cgcignore that restates its .gitignore. Patterns are layered defaults -> .gitignore -> .cgcignore. Matching is last-match-wins, so a negated pattern in .cgcignore can still bring a git-ignored path back into the graph. Fixes #729 Signed-off-by: Aloys Jehwin <[email protected]> * normalize module-node label to the plain filename in all render sites --------- Signed-off-by: Aloys Jehwin <[email protected]> Co-authored-by: Donovan Yohan <[email protected]> Co-authored-by: Aloys Jehwin <[email protected]> Co-authored-by: Shashank Shekhar Singh <[email protected]>

* fix: find functions by argument type * fix(jobs): serialize last update time in job responses (#1679) * fix(cli): explain embedded database lock conflicts (#1684) * fix(setup-wizard): stop replacing IDE settings that are JSONC (#1677) VS Code and its forks write settings.json as JSONC. json.load rejects comments and trailing commas, and the wizard treated that rejection as "no settings yet" before writing the file back, so a user's whole configuration was replaced by a lone mcpServers key. Parse JSONC before giving up, and if the file still cannot be parsed, leave it alone instead of overwriting it. Back up the file before writing either way, and say so when comments are present, since json.dump cannot preserve them. Fixes #660 Signed-off-by: Aloys Jehwin <[email protected]> * feat(cgcignore): treat .gitignore as an ignore source (#1680) Anything git ignores is now ignored by the indexer, so a repository no longer needs a .cgcignore that restates its .gitignore. Patterns are layered defaults -> .gitignore -> .cgcignore. Matching is last-match-wins, so a negated pattern in .cgcignore can still bring a git-ignored path back into the graph. Fixes #729 Signed-off-by: Aloys Jehwin <[email protected]> * fix(viz): display source filenames for synthetic module nodes (#1682) * fix(viz): display source filenames for synthetic module nodes * fix(jobs): serialize last update time in job responses (#1679) * fix(cli): explain embedded database lock conflicts (#1684) * fix(setup-wizard): stop replacing IDE settings that are JSONC (#1677) VS Code and its forks write settings.json as JSONC. json.load rejects comments and trailing commas, and the wizard treated that rejection as "no settings yet" before writing the file back, so a user's whole configuration was replaced by a lone mcpServers key. Parse JSONC before giving up, and if the file still cannot be parsed, leave it alone instead of overwriting it. Back up the file before writing either way, and say so when comments are present, since json.dump cannot preserve them. Fixes #660 Signed-off-by: Aloys Jehwin <[email protected]> * feat(cgcignore): treat .gitignore as an ignore source (#1680) Anything git ignores is now ignored by the indexer, so a repository no longer needs a .cgcignore that restates its .gitignore. Patterns are layered defaults -> .gitignore -> .cgcignore. Matching is last-match-wins, so a negated pattern in .cgcignore can still bring a git-ignored path back into the graph. Fixes #729 Signed-off-by: Aloys Jehwin <[email protected]> * normalize module-node label to the plain filename in all render sites --------- Signed-off-by: Aloys Jehwin <[email protected]> Co-authored-by: Donovan Yohan <[email protected]> Co-authored-by: Aloys Jehwin <[email protected]> Co-authored-by: Shashank Shekhar Singh <[email protected]> * fix the argument query so it filters f; behavioral pin on real kuzu --------- Signed-off-by: Aloys Jehwin <[email protected]> Co-authored-by: Donovan Yohan <[email protected]> Co-authored-by: Aloys Jehwin <[email protected]> Co-authored-by: Upanshi Mittal <[email protected]> Co-authored-by: Shashank Shekhar Singh <[email protected]>

…1676) * feat: add SSL connection parameters to cassandra_ingester.py * feat: add SSL connection parameters to mysql_ingester.py * fix(jobs): serialize last update time in job responses (#1679) * fix(cli): explain embedded database lock conflicts (#1684) * fix(setup-wizard): stop replacing IDE settings that are JSONC (#1677) VS Code and its forks write settings.json as JSONC. json.load rejects comments and trailing commas, and the wizard treated that rejection as "no settings yet" before writing the file back, so a user's whole configuration was replaced by a lone mcpServers key. Parse JSONC before giving up, and if the file still cannot be parsed, leave it alone instead of overwriting it. Back up the file before writing either way, and say so when comments are present, since json.dump cannot preserve them. Fixes #660 Signed-off-by: Aloys Jehwin <[email protected]> * feat(cgcignore): treat .gitignore as an ignore source (#1680) Anything git ignores is now ignored by the indexer, so a repository no longer needs a .cgcignore that restates its .gitignore. Patterns are layered defaults -> .gitignore -> .cgcignore. Matching is last-match-wins, so a negated pattern in .cgcignore can still bring a git-ignored path back into the graph. Fixes #729 Signed-off-by: Aloys Jehwin <[email protected]> * fix(viz): display source filenames for synthetic module nodes (#1682) * fix(viz): display source filenames for synthetic module nodes * fix(jobs): serialize last update time in job responses (#1679) * fix(cli): explain embedded database lock conflicts (#1684) * fix(setup-wizard): stop replacing IDE settings that are JSONC (#1677) VS Code and its forks write settings.json as JSONC. json.load rejects comments and trailing commas, and the wizard treated that rejection as "no settings yet" before writing the file back, so a user's whole configuration was replaced by a lone mcpServers key. Parse JSONC before giving up, and if the file still cannot be parsed, leave it alone instead of overwriting it. Back up the file before writing either way, and say so when comments are present, since json.dump cannot preserve them. Fixes #660 Signed-off-by: Aloys Jehwin <[email protected]> * feat(cgcignore): treat .gitignore as an ignore source (#1680) Anything git ignores is now ignored by the indexer, so a repository no longer needs a .cgcignore that restates its .gitignore. Patterns are layered defaults -> .gitignore -> .cgcignore. Matching is last-match-wins, so a negated pattern in .cgcignore can still bring a git-ignored path back into the graph. Fixes #729 Signed-off-by: Aloys Jehwin <[email protected]> * normalize module-node label to the plain filename in all render sites --------- Signed-off-by: Aloys Jehwin <[email protected]> Co-authored-by: Donovan Yohan <[email protected]> Co-authored-by: Aloys Jehwin <[email protected]> Co-authored-by: Shashank Shekhar Singh <[email protected]> * fix: find functions by argument type (#1686) * fix: find functions by argument type * fix(jobs): serialize last update time in job responses (#1679) * fix(cli): explain embedded database lock conflicts (#1684) * fix(setup-wizard): stop replacing IDE settings that are JSONC (#1677) VS Code and its forks write settings.json as JSONC. json.load rejects comments and trailing commas, and the wizard treated that rejection as "no settings yet" before writing the file back, so a user's whole configuration was replaced by a lone mcpServers key. Parse JSONC before giving up, and if the file still cannot be parsed, leave it alone instead of overwriting it. Back up the file before writing either way, and say so when comments are present, since json.dump cannot preserve them. Fixes #660 Signed-off-by: Aloys Jehwin <[email protected]> * feat(cgcignore): treat .gitignore as an ignore source (#1680) Anything git ignores is now ignored by the indexer, so a repository no longer needs a .cgcignore that restates its .gitignore. Patterns are layered defaults -> .gitignore -> .cgcignore. Matching is last-match-wins, so a negated pattern in .cgcignore can still bring a git-ignored path back into the graph. Fixes #729 Signed-off-by: Aloys Jehwin <[email protected]> * fix(viz): display source filenames for synthetic module nodes (#1682) * fix(viz): display source filenames for synthetic module nodes * fix(jobs): serialize last update time in job responses (#1679) * fix(cli): explain embedded database lock conflicts (#1684) * fix(setup-wizard): stop replacing IDE settings that are JSONC (#1677) VS Code and its forks write settings.json as JSONC. json.load rejects comments and trailing commas, and the wizard treated that rejection as "no settings yet" before writing the file back, so a user's whole configuration was replaced by a lone mcpServers key. Parse JSONC before giving up, and if the file still cannot be parsed, leave it alone instead of overwriting it. Back up the file before writing either way, and say so when comments are present, since json.dump cannot preserve them. Fixes #660 Signed-off-by: Aloys Jehwin <[email protected]> * feat(cgcignore): treat .gitignore as an ignore source (#1680) Anything git ignores is now ignored by the indexer, so a repository no longer needs a .cgcignore that restates its .gitignore. Patterns are layered defaults -> .gitignore -> .cgcignore. Matching is last-match-wins, so a negated pattern in .cgcignore can still bring a git-ignored path back into the graph. Fixes #729 Signed-off-by: Aloys Jehwin <[email protected]> * normalize module-node label to the plain filename in all render sites --------- Signed-off-by: Aloys Jehwin <[email protected]> Co-authored-by: Donovan Yohan <[email protected]> Co-authored-by: Aloys Jehwin <[email protected]> Co-authored-by: Shashank Shekhar Singh <[email protected]> * fix the argument query so it filters f; behavioral pin on real kuzu --------- Signed-off-by: Aloys Jehwin <[email protected]> Co-authored-by: Donovan Yohan <[email protected]> Co-authored-by: Aloys Jehwin <[email protected]> Co-authored-by: Upanshi Mittal <[email protected]> Co-authored-by: Shashank Shekhar Singh <[email protected]> * fix(viz): render FalkorDB relationships in the live graph (#1689) parse_element classified relationships by class name, matching only Relationship/KuzuRelationship. FalkorDB's edge class is named Edge, so it matched no branch and every FalkorDB relationship was silently dropped — on the backend that is CGC's default on Unix under Python 3.12+. parse_rel directly below already reads FalkorDB edges correctly; it was never reached. The offline renderer in cli_helpers already classified by duck typing and handled this (#1453). Both renderers now share those predicates in utils/graph_shapes, so classification cannot drift apart again. * expose --ssl-verify/--ssl-ca-certs on the datasource CLI; test the driver kwargs --------- Signed-off-by: Aloys Jehwin <[email protected]> Co-authored-by: Donovan Yohan <[email protected]> Co-authored-by: Aloys Jehwin <[email protected]> Co-authored-by: Upanshi Mittal <[email protected]> Co-authored-by: Shashank Shekhar Singh <[email protected]> Co-authored-by: Mansurshakh Japarov <[email protected]> Co-authored-by: Abhinav Singh <[email protected]>

…1567) (#1694) Every entry is sourced from an actual issue (#1673 census loop, #1683 lock conflicts, #1317 context desync, #1597 silent vector resolve, #1625 stale grammar venv, #1677 JSONC settings, #1680 ignore layering, #1685 arg types, #1689 missing viz edges), with the version each fix shipped in and the still-applicable workarounds. Linked from the README.

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AloysJehwin mentioned this pull request Aug 27, 2026

Installation of CodeGraphContext overwrites VS Code settings #660

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Shashankss1205 approved these changes Sep 2, 2026

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Shashankss1205 merged commit 5f3f208 into CodeGraphContext:main Sep 2, 2026
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github-project-automation Bot moved this from Backlog tasks to Done in CGC Progress Board Sep 2, 2026

This was referenced Sep 2, 2026

chore(release): bump version to 0.6.9 #1690

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docs: TROUBLESHOOTING.md sourced from real reported issues (#1567) #1694

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Shashankss1205 mentioned this pull request Sep 6, 2026

fix(code-finder): match find_functions_by_argument against arg_types not parameter names #1701

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fix(setup-wizard): stop replacing IDE settings that are JSONC - #1677

fix(setup-wizard): stop replacing IDE settings that are JSONC#1677
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AloysJehwin:fix/preserve-jsonc-ide-settings

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