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Shorten w3id prefix, stage redirect, dogfood #30 on SPRUCE (#79)
* Shorten w3id prefix, stage redirect, and dogfood #30 on SPRUCE Closes #12 by staging the upstream w3id.org redirect for https://w3id.org/communitymech/ (apply by copying w3id/communitymech/ into a fork of perma-id/w3id.org). The LinkML schema prefix is shortened from /culturebot-ai/communitymech/ to /communitymech/ so the registered redirect resolves CommunityMech CURIEs, and the generated datamodel and SPARQL examples are updated to match. Also adds the first dogfood use of #30's cross-repo linking schema: SPRUCE peatland community now declares humic-substance electron acceptors and acetate as related_ingredients, anchored to existing PMID:40715043 evidence. No MediaIngredientMech IDs minted yet; this exercises the schema using preferred_term + CHEBI + evidence only, which is the dogfood pattern recommended in cross_repo_linking.md. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * Format regenerated datamodel with black Addresses Copilot review feedback on #79: the regenerated LinkML datamodel didn't match the repo's black formatting (line length 100, default string normalization), so `just lint`'s `black --check` would flag it. Running `just format` reformats only this file; the rest of src/ and tests/ is untouched and `black --check src/ tests/` now reports all 46 files clean. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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‎docs/cross_repo_linking.md‎

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### SPARQL: Find Media for Peatland Communities
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```sparql
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PREFIX cm: <https://w3id.org/culturebot-ai/communitymech/>
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PREFIX cm: <https://w3id.org/communitymech/>
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SELECT ?community_name ?media_name ?culturemech_id ?relationship
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WHERE {
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### SPARQL: Find Ingredients for an Environment
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```sparql
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PREFIX cm: <https://w3id.org/culturebot-ai/communitymech/>
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PREFIX cm: <https://w3id.org/communitymech/>
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SELECT ?community_name ?ingredient ?mim_id ?relevance
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WHERE {
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### SPARQL: Full Cross-Repo Join via Shared ENVO Terms
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```sparql
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PREFIX cm: <https://w3id.org/culturebot-ai/communitymech/>
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PREFIX cm: <https://w3id.org/communitymech/>
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PREFIX cult: <https://w3id.org/culturebot-ai/culturemech/>
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PREFIX mim: <https://w3id.org/culturebot-ai/mediaingredientmech/>
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### SPARQL: Reverse Lookup -- Communities for a CultureMech Medium
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```sparql
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PREFIX cm: <https://w3id.org/culturebot-ai/communitymech/>
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PREFIX cm: <https://w3id.org/communitymech/>
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SELECT ?community_name ?environment ?relationship
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WHERE {

‎kb/communities/SPRUCE_Peatland_Methane_Cycling_Community.yaml‎

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to the peatland's CH4/CO2 carbon-chemistry gradient and depth/water structure -
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reinforcing peat chemistry (alongside the existing pH/TOC quantification) as a
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principal driver of community composition.
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related_ingredients:
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- preferred_term: humic substances
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chebi_term:
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id: CHEBI:34818
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label: humic acid
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relevance: Peat soil organic matter serves as an electron-acceptor pool that
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sustains anaerobic respiration alongside methanogenesis at SPRUCE; humic
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substances are the dominant electron-accepting fraction of that pool.
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evidence:
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- reference: PMID:40715043
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supports: SUPPORT
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evidence_source: COMPUTATIONAL
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snippet: acquire electron acceptors from soil organic matter
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explanation: The paper's headline claim links the SPRUCE peat microbial
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community to soil-organic-matter electron acceptors, the humic-substance
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fraction of which would anchor any environment-analog medium for this
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community.
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- preferred_term: acetate
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chebi_term:
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id: CHEBI:30089
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label: acetate
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relevance: Acetate accumulates in deep peat from acetogenic Wood-Ljungdahl
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activity and is the dominant substrate for acetoclastic methanogenesis at
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the bog surface, so any cultivation medium designed around SPRUCE
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methanogens would need acetate as a primary carbon and energy source.
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evidence:
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- reference: PMID:40715043
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supports: SUPPORT
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evidence_source: COMPUTATIONAL
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snippet: the genomic potential for acetogenesis via the Wood-Ljungdahl pathway
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continues to increase, resulting in the highest concentrations of acetate
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in the deep peat
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explanation: Anchors acetate as the dominant environmentally relevant
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organic acid in SPRUCE peat porewater.
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associated_datasets:
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- name: SPRUCE peat metagenomes
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dataset_type: METAGENOME

‎src/communitymech/datamodel/communitymech.py‎

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# Auto generated from communitymech.yaml by pythongen.py version: 0.0.1
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# Generation date: 2026-05-16T01:52:45
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# Generation date: 2026-05-23T01:23:35
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# Schema: communitymech
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#
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# id: https://w3id.org/culturebot-ai/communitymech
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# id: https://w3id.org/communitymech
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# description: Schema for modeling microbial community structure, function, and ecological interactions
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# license: BSD-3-Clause
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NCBITAXON = CurieNamespace("NCBITaxon", "http://purl.obolibrary.org/obo/NCBITaxon_")
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PMID = CurieNamespace("PMID", "http://www.ncbi.nlm.nih.gov/pubmed/")
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UBERON = CurieNamespace("UBERON", "http://purl.obolibrary.org/obo/UBERON_")
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COMMUNITYMECH = CurieNamespace("communitymech", "https://w3id.org/culturebot-ai/communitymech/")
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COMMUNITYMECH = CurieNamespace("communitymech", "https://w3id.org/communitymech/")
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DOI = CurieNamespace("doi", "https://doi.org/")
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LINKML = CurieNamespace("linkml", "https://w3id.org/linkml/")
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XSD = CurieNamespace("xsd", "http://www.w3.org/2001/XMLSchema#")

‎src/communitymech/schema/communitymech.yaml‎

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id: https://w3id.org/culturebot-ai/communitymech
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id: https://w3id.org/communitymech
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name: communitymech
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title: Microbial Community Mechanisms Knowledge Base Schema
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description: Schema for modeling microbial community structure, function, and ecological interactions
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prefixes:
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linkml: https://w3id.org/linkml/
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communitymech: https://w3id.org/culturebot-ai/communitymech/
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communitymech: https://w3id.org/communitymech/
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NCBITaxon: http://purl.obolibrary.org/obo/NCBITaxon_
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ENVO: http://purl.obolibrary.org/obo/ENVO_
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CHEBI: http://purl.obolibrary.org/obo/CHEBI_

‎w3id/README.md‎

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# w3id.org redirect for CommunityMech
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This directory stages the upstream pull request to
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[perma-id/w3id.org](https://github.com/perma-id/w3id.org) that registers
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`https://w3id.org/communitymech/` as a permanent identifier prefix for
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CommunityMech CURIEs.
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## Files
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- `communitymech/.htaccess` — redirect rules. Copy verbatim to
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`communitymech/.htaccess` in a fork of `perma-id/w3id.org` and open a PR.
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## Resolution targets
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| URL | Target |
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|--------------------------------------------------------------|-------------------------------------------------------------------------------------------|
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| `https://w3id.org/communitymech/` | `https://culturebotai.github.io/CommunityMech/` |
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| `https://w3id.org/communitymech/<Name>` | `https://culturebotai.github.io/CommunityMech/communities/<Name>.html` |
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| `https://w3id.org/communitymech/<Name>.html` | same as above |
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| `https://w3id.org/communitymech/<Name>.yaml` | `https://raw.githubusercontent.com/CultureBotAI/CommunityMech/main/kb/communities/<Name>.yaml` |
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| `https://w3id.org/communitymech/schema/communitymech.yaml` | `https://raw.githubusercontent.com/CultureBotAI/CommunityMech/main/src/communitymech/schema/communitymech.yaml` |
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`<Name>` is the community filename slug (e.g., `EcoFAB_Ring_Trial_SynCom17`)
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that matches `kb/communities/<Name>.yaml`. CommunityMech also assigns each
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record a numeric identifier (`CommunityMech:NNNNNN`) which is recorded in
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the YAML body but not used as the URL path component.
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## Schema prefix update
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The LinkML schema's `communitymech` prefix was shortened from
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`https://w3id.org/culturebot-ai/communitymech/` to
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`https://w3id.org/communitymech/` in the same change that added this
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directory, so that the registered redirect matches the schema.
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## Submission
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1. Fork `perma-id/w3id.org`.
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2. Copy `communitymech/` from this directory into the fork root.
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3. Open a PR following the contribution guidelines in that repo
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(`CONTRIBUTING.md`). Use this directory's README as PR context.
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Issue: [CultureBotAI/CommunityMech#12](https://github.com/CultureBotAI/CommunityMech/issues/12)

‎w3id/communitymech/.htaccess‎

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# Redirect rules for https://w3id.org/communitymech/
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#
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# Owner: CultureBotAI (https://github.com/CultureBotAI)
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# Contact: marcinjoachimiak@gmail.com
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# Source repo: https://github.com/CultureBotAI/CommunityMech
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#
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# Pattern summary:
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# / -> CommunityMech docs landing page
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# /<Name> -> Per-community HTML page on github.io
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# /<Name>.html -> Same as /<Name>, idempotent
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# /<Name>.yaml -> Source YAML on GitHub raw
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# /schema/communitymech.yaml -> LinkML schema source
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#
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# CommunityMech identifiers in the LinkML schema use the CURIE form
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# `CommunityMech:NNNNNN` (e.g., CommunityMech:000024). The community
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# slug (filename without .yaml) is what resolves here; the numeric ID
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# is recorded in the YAML body. See the project's docs for the mapping.
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Options +FollowSymLinks
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RewriteEngine On
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# Schema source
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RewriteRule ^schema/communitymech\.yaml$ https://raw.githubusercontent.com/CultureBotAI/CommunityMech/main/src/communitymech/schema/communitymech.yaml [R=302,L]
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# Per-community source YAML
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RewriteRule ^([A-Za-z0-9_]+)\.yaml$ https://raw.githubusercontent.com/CultureBotAI/CommunityMech/main/kb/communities/$1.yaml [R=302,L]
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# Per-community HTML page (canonical)
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RewriteRule ^([A-Za-z0-9_]+)\.html$ https://culturebotai.github.io/CommunityMech/communities/$1.html [R=302,L]
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# Per-community HTML page (extensionless CURIE local part)
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RewriteRule ^([A-Za-z0-9_]+)$ https://culturebotai.github.io/CommunityMech/communities/$1.html [R=302,L]
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# Landing page
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RewriteRule ^$ https://culturebotai.github.io/CommunityMech/ [R=302,L]

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